Gene Expression Studies

Source Tissue Test Condition Control Condition Keywords description test_size control_size dbxref
GEO:GSE30915-1 trophoblast BMP4-treated human embryonic stem cells at day 2 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE14771|A1 blood third trimester pregnancy non-pregnant female [maternal blood normal pregnancy third trimester gestational age] Heung et al. investigated the detection of fetal mRNA in maternal whole blood to determine if it offered advantages over maternal plasma analysis. Peripheral blood samples were collected from 5 third-trimester healthy women with singleton uncomplicated pregnancies (38–39 weeks) and 5 age-matched healthy non-pregnant females. 5 5 PMID:19516908
GEO:GPL96
GEO:GSE14771
ProteinAtlas - cell line: HeLa HeLa cell [cell line HeLa] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999[A]-6 decidua basal plate at 23–24 weeks basal plate at 18–19 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE27272-2 umbilical cord blood non-smoker smoker [placenta prenatal tobacco exposure smoking] Votavova et al. performed a comprehensive analysis of transcriptome alterations induced by smoking in maternal and fetal cells. Samples of peripheral blood, placenta, and cord blood were obtained from pregnant smokers and gravidas without significant exposure to tobacco smoke. Smoking status was confirmed by detection of excessive plasma levels of cotinine. Placental samples were prepared according to the protocol by Sood et al., as described in detail previously. 17 37 PMID:21803418
GEO:GPL6883
GEO:GSE27272
ProteinAtlas - tissue: skeletal muscle skeletal muscle tissue [tissue skeletal muscle] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE40182|3 cytotrophoblast preeclampsia cytotrophoblasts at 24 hours preterm labor cytotrophoblasts at 24 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE31976|4 blood non-Treg cells from maternal blood Treg cells from maternal blood [maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 5 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE42112-1 cytotrophoblast primary human placental cells (HLA-G−/TACSTD2+) primary human placental cells (HLA-G+) [cytotrophoblasts extravillous trophoblasts embryonic stem cells cell culture] Telugu et al. compared extravillous trophoblast (EVT) cells derived from human embryonic stem cells (hESC) to those obtained from first trimester human placentas in order to evaluate their potential as an in vitro model for investigating EVT invasion. HESC were treated with BMP4 under 4% or 20% oxygen and tested in Matrigel invasion chambers. Both BMP4-treated hESC and primary human placental cells were separated into HLA-G+ (EVT) and HLA-G−/TACSTD2+ (cytotrophoblast) populations with immunomagnetic beads and expression profiles analyzed by microarray. 3 3 PMID:23631809
GEO:GPL13497
GEO:GSE42112
GEO:GSE5999|A1 decidua 18-19 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE5809-2 endometrial stroma TCM-treated human endometrial stromal cells at 12 hours CCM-treated human endometrial stromal cells at 12 hours [endometrial stromal cells decidualization cell culture] To investigate paracrine communications that occur at the decidua-trophoblast interface, Hess et al. studied the effects of products secreted from human trophoblasts on global gene expression in in vitro-decidualized human endometrial stromal cells. Human endometrial stromal cells were decidualized with progesterone and cultured in human trophoblast-conditioned media (TCM), or in conditioned media from non-decidualized stromal cells (CCM) as a control. 2 3 PMID:17021345
GEO:GPL570
GEO:GSE5809
GEO:GSE31976-7 umbilical cord blood non-Treg cells from cord blood Treg cells from cord blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE7676-1 placenta Pcdh12−/− placenta wild-type control [placenta gene knockout] Although alive and fertile, protocadherin-12 (Pcdh12)-deficient mice exhibit two major morphological modifications in their placental phenotype: decreased vascular and cell densities in the labyrinth and a missegregation of the labyrinthine and the junctional zone. To understand the molecular events responsible for these alterations observed in Pcdh12−/− placentas, Rampon et al. performed gene expression profiling on embryonic day 12.5 mutant placentas compared with wild-type placentas. 5 5 PMID:18477666
GEO:GPL1261
GEO:GSE7676
GEO:GSE38095-3 placenta 50% food restriction with leptin replacement 50% food restriction [placenta leptin maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed, 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two placentas from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
GEO:GSE46510-4 blood term delivery spontaneous preterm birth within 48 hours [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE5999[A]-7 decidua basal plate at 37–40 weeks basal plate at 18–19 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE7586-1 chorionic villus acute placental malaria (no inflammation) uninfected control (no inflammation) [placenta infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 3 9 PMID:17579077
GEO:GPL570
GEO:GSE7586
ProteinAtlas - cell line: U-2 OS U2-OS cell [cell line U-2 OS] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE7586|3 chorionic villus chronic placental malaria (inflammation) acute placental malaria (no inflammation) [placenta inflammation infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 7 3 PMID:17579077
GEO:GPL570
GEO:GSE7586
GEO:GSE23339-1 endometrium endometrioma control endometrium [endometrium endometrioma endometriosis] To begin to understand the pathogenesis of endometriomas, Hawkins et al. carried out the first transcriptome-microRNAome analysis of endometriomas and eutopic endometrium and used gene expression profiling on the same samples to determine functional targets for these microRNA. Specimens were collected from women undergoing clinically indicated gynecologic surgery for removal of an endometriotic mass and/or other benign indications. Specimens of endometrium were obtained from the uterine fundus at the time of hysterectomy at a distance from any uterine leiomyomata. Specimens of endometriomas were full-thickness 1 cm biopsies of the cyst wall and were isolated away from areas of obvious ovarian cortex. 10 9 PMID:21436257
GEO:GPL6102
GEO:GSE23339
ProteinAtlas - cell line: U-2197 cell culture [cell line U-2197] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: small intestine small intestine [tissue small intestine] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE48521-1 amniotic fluid obese mother lean mother [amniotic fluid maternal nutrition maternal obesity] To investigate fetal gene expression in obese women compared to lean women in the second trimester, Edlow et al. performed global gene expression analysis of amniotic fluid cell-free RNA. Samples were collected from women with a BMI ≥30 (obese) or <25 (lean) undergoing second trimester (14–24 weeks) genetic amniocentesis. Fetuses later found to have an abnormal karyotype were excluded from the study. 8 8 PMID:24558408
GEO:GPL570
GEO:GSE48521
GEO:GSE30186-1 chorionic villus preeclamptic pregnancy normal pregnancy [chorionic villus prelabor cesarean section preeclampsia] Meng et al. performed a comprehensive analysis of gene expression profiles in placentas from preeclamptic pregnancies versus normal placentas. Placental tissues were obtained immediately after delivery from women with normal pregnancies and patients with preeclampsia. Preeclampsia was diagnosed when both pregnancyinduced hypertension and proteinuria were present. All women were delivered via elective cesarean delivery without labor to eliminate the effect of labor. Tissue blocks (approximately 1 cm³ each) were dissected from the standard locations on the maternal face of the placentas as previously described by Sood et al., 2006. Villous portions were harvested by dissecting free of blood vessels and connective tissue and washing off adherent blood clots. 6 6 PMID:22702245
GEO:GPL10558
GEO:GSE30186
GEO:GSE40182-2 cytotrophoblast preeclampsia cytotrophoblasts at 12 hours preterm labor cytotrophoblasts at 12 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE65265-1 uterine cervix pregnant cervix with Mφs nonpregnant cervix with Mφs [uterine cervix tissue macrophages] To test the hypothesis that expression of genes unique to resident macrophages (Mφs) distinguishes the late remodeled prepartum from unremodeled nonpregnant cervix, Dobyns et al. performed a microarray analysis on perfused cervix, with or without Mφs, from prepartum day 21 postbreeding and nonpregnant rats. Cells from the cervix in the macrophage-depleted groups were subjected to a magnetic bead separation procedure to remove Mφs. 3 3 PMID:25811906
GEO:GPL14746
GEO:GSE65265
ProteinAtlas - cell line: U-698 cell culture [cell line U-698] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE46510-7 blood term delivery preterm birth after 7 days [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 15 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE5999|B1 decidua 18-19 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE65265-3 uterine cervix pregnant cervix without Mφs pregnant cervix with Mφs [uterine cervix tissue macrophages] To test the hypothesis that expression of genes unique to resident macrophages (Mφs) distinguishes the late remodeled prepartum from unremodeled nonpregnant cervix, Dobyns et al. performed a microarray analysis on perfused cervix, with or without Mφs, from prepartum day 21 postbreeding and nonpregnant rats. Cells from the cervix in the macrophage-depleted groups were subjected to a magnetic bead separation procedure to remove Mφs. 3 3 PMID:25811906
GEO:GPL14746
GEO:GSE65265
GEO:GSE31976|3 blood non-Treg cells from maternal blood non-Treg cells from non-pregnant control [maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
ProteinAtlas - cell line: Daudi DAUDI cell [cell line Daudi] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE53669-2 umbilical cord blood postpartum maternal blood antepartum maternal blood [maternal blood normal pregnancy postpartum antepartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 12 12 PMID:17885688
GEO:GPL96
GEO:GSE53669
ProteinAtlas - tissue: pancreas pancreas [tissue pancreas] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE40182|2 cytotrophoblast preeclampsia cytotrophoblasts at 12 hours preterm labor cytotrophoblasts at 12 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
ProteinAtlas - cell line: REH REH cell [cell line REH] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE63901-1 endometrium out-of-phase endometrial histology normal endometrial histology [endometrium recurrent miscarriage recurrent early pregnancy loss] Kosova et al. characterized gene expression profiles of midsecretory endometria from women with recurrent early pregnancy loss. The study included 32 women of European ancestry with two or more documented unexplained miscarriages, who were classified into three groups based on endometrial histological dating and cyclin E levels. Abnormal endometrial histologies and abnormal cyclin E levels were defined as ≥3 days of endometrial developmental delay and >20% expression in the endometrial glandular cells, respectively. All women had endometrial biopsies performed during their mid-luteal phase, 9–11 days following the endogenous LH surge. For 5 additional women with elevated cyclin E levels, biopsy samples were collected in the mid-luteal phase both prior to and post-progesterone treatment to investigate the gene expression profiles in response to treatment. 20 44 PMID:25586782
GEO:GPL10558
GEO:GSE63901
ProteinAtlas - cell line: HEL HEL cell [cell line HEL] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE9984|2 chorionic villus third trimester pregnancy first trimester pregnancy [placenta normal pregnancy third trimester elective termination first trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45-59 days) and second trimester (109-115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the termination or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
GEO:GSE48424|2 blood severe preeclampsia normal pregnancy [maternal blood severe preeclampsia preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia (PE). The study included 13 women with severe PE, 6 women with non-severe PE, and 19 women with normal pregnancies. The diagnosis of PE was based on changes in blood pressure, proteinuria and increased uricemia. 12 18 PMID:24349325
GEO:GPL6480
GEO:GSE48424
GEO:GSE56899-3 blood plasma third trimester pregnancy non-pregnant control [maternal plasma normal pregnancy third trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE5999|A8 decidua 23-24 weeks pregnant 21 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE56899-8 blood plasma third trimester pregnancy second trimester pregnancy [maternal plasma normal pregnancy third trimester second trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE46510|7 blood term delivery preterm birth at >7 days and <37 weeks [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 15 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE5999[B]-9 decidua basal plate at 37–40 weeks basal plate at 21 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE5999|A10 decidua 37-40 weeks pregnant 23-24 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE5999|A2 decidua 21 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - cell line: SiHa SiHa cell [cell line SiHa] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE40636-1 umbilical cord blood peptidoglycan-treated neutrophils untreated control [umbilical cord blood neutrophils immune challenge cell culture] Fong et al. employed whole genome microarray expression profiling to investigate the mechanism of response to peptidoglycan in neonatal neutrophils. Umbilical cord blood samples were collected after normal term vaginal deliveries, and isolated neutrophils were treated with 10 g/ml peptidoglycan or with medium only for 4 hours. 3 3 PMID:23986550
GEO:GPL570
GEO:GSE40636
ProteinAtlas - tissue: appendix vermiform appendix [tissue appendix] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE42112-2 cytotrophoblast BMP4-treated human embryonic stem cells (HLA-G−/TACSTD2+) BMP4-treated human embryonic stem cells (HLA-G+) [cytotrophoblasts extravillous trophoblasts embryonic stem cells cell culture] Telugu et al. compared extravillous trophoblast (EVT) cells derived from human embryonic stem cells (hESC) to those obtained from first trimester human placentas in order to evaluate their potential as an in vitro model for investigating EVT invasion. HESC were treated with BMP4 under 4% or 20% oxygen and tested in Matrigel invasion chambers. Both BMP4-treated hESC and primary human placental cells were separated into HLA-G+ (EVT) and HLA-G−/TACSTD2+ (cytotrophoblast) populations with immunomagnetic beads and expression profiles analyzed by microarray. 3 3 PMID:23631809
GEO:GPL13497
GEO:GSE42112
GEO:GSE5999[B]-2 decidua basal plate at 21 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE53669-3 umbilical cord blood postpartum maternal blood umbilical cord blood [umbilical cord blood maternal blood normal pregnancy postpartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 12 13 PMID:17885688
GEO:GPL96
GEO:GSE53669
ProteinAtlas - cell line: CACO-2 CACO-2 cell [cell line CACO-2] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE56899-7 blood plasma postpartum first trimester pregnancy [maternal plasma normal pregnancy postpartum first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE46510-5 blood preterm birth after 7 days preterm birth after 48 hours and within 7 days [maternal blood preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 15 12 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE56899|8 blood plasma postpartum third trimester pregnancy [maternal plasma normal pregnancy postpartum third trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE7586|1 chorionic villus acute placental malaria (no inflammation) uninfected control (no inflammation) [placenta inflammation infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 3 9 PMID:17579077
GEO:GPL570
GEO:GSE7586
GEO:GSE14722|B1 decidua preeclampsia basal plate biopsy preterm basal plate biopsy [basal plate preterm labor preeclampsia] Winn et al. conducted a global analysis of gene expression at the maternal-fetal interface in placental samples from women with preeclampsia versus samples from women who delivered due to preterm labor with no evidence of infection. The basal plate was dissected from the placenta proper and diced into approximately 3 mmᶾ pieces, which were snap frozen in liquid nitrogen and stored at −70 °C. Pregnancies complicated by multiple gestations, fetal anomalies, premature rupture of the membranes, infection, diabetes, or other autoimmune diseases were excluded. 12 11 PMID:18818296
GEO:GPL97
GEO:GSE14722
GEO:GSE46510|2 blood preterm birth after 48 hours and within 7 days spontaneous preterm birth within 48 hours [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 12 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE38095|1 placenta 50% food restriction ad libitum fed [placenta leptin maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed (control), 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
GEO:GSE63901|1 endometrium out-of-phase endometrial histology normal endometrial histology [endometrium progesterone drug treatment recurrent miscarriage recurrent early pregnancy loss] Kosova et al. characterized gene expression profiles of midsecretory endometria from women with recurrent early pregnancy loss. The study included 32 women of European ancestry with two or more documented unexplained miscarriages, who were classified into three groups based on endometrial histological dating and cyclin E levels. Abnormal endometrial histologies and abnormal cyclin E levels were defined as ≥3 days of endometrial developmental delay and >20% expression in the endometrial glandular cells, respectively. All women had endometrial biopsies performed during their mid-luteal phase, 9-11 days following the endogenous LH surge. For 5 additional women with elevated cyclin E levels, biopsy samples were collected in the mid-luteal phase both prior to and post-progesterone treatment to investigate the gene expression profiles in response to treatment. 20 44 PMID:25586782
GEO:GPL10558
GEO:GSE63901
GEO:GSE40182-3 cytotrophoblast preeclampsia cytotrophoblasts at 24 hours preterm labor cytotrophoblasts at 24 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE7971|1 corpus luteum PGF2α treatment vehicle treatment [corpus luteum luteolysis drug treatment] To delineate the mechanism of PGF2α-induced luteolysis, Priyanka et al. studied the global changes in gene expression within the corpus luteum following PGF2α treatment of female bonnet monkeys. PGF2α or PBS (vehicle) was administered to female monkeys via three injections on day 10 of the luteal phase. At 24 hours following either PGF2α or PBS administration, corpus luteum samples were collected, immediately cut into 4-5 pieces, and snap frozen in liquid nitrogen. 3 3 PMID:18988674
GEO:GPL3535
GEO:GSE7971
GEO:GSE38095|3 placenta 50% food restriction with leptin replacement 50% food restriction [placenta leptin maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed (control), 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
ProteinAtlas - tissue: duodenum duodenum [tissue duodenum] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: HDLM-2 cell culture [cell line HDLM-2] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: adipose tissue adipose tissue [tissue adipose tissue] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE63901|3 endometrium post-progesterone treatment pre-progesterone treatment [endometrium progesterone drug treatment recurrent miscarriage recurrent early pregnancy loss] Kosova et al. characterized gene expression profiles of midsecretory endometria from women with recurrent early pregnancy loss. The study included 32 women of European ancestry with two or more documented unexplained miscarriages, who were classified into three groups based on endometrial histological dating and cyclin E levels. Abnormal endometrial histologies and abnormal cyclin E levels were defined as ≥3 days of endometrial developmental delay and >20% expression in the endometrial glandular cells, respectively. All women had endometrial biopsies performed during their mid-luteal phase, 9-11 days following the endogenous LH surge. For 5 additional women with elevated cyclin E levels, biopsy samples were collected in the mid-luteal phase both prior to and post-progesterone treatment to investigate the gene expression profiles in response to treatment. 10 10 PMID:25586782
GEO:GPL10558
GEO:GSE63901
GEO:GSE61822-1 chorion neurocognitive impairment no neurocognitive impairment [chorioamniotic membrane preterm birth neurocognitive impairment] Pappas et al. conducted a retrospective case-control microarray study that characterized the chorioamniotic membranes of preterm neonates with or without neurocognitive impairment at 18–24 months. Chorioamniotic membrane samples were retrieved from the biological sample bank of Wayne State University and the Perinatology Research Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development. Cases and controls were singleton neonates born between 23–32 weeks of gestation matched for gestational age. Neurocognitive impairment was defined by a cognitive composite score of <80 with or without associated neuromotor impairment at 18–24 months’ corrected age according to the Bayley Scales of Infant Development, 3rd Edition. 14 14 PMID:25822971
GEO:GPL10558
GEO:GSE61822
GEO:GSE39840-1 umbilical cord blood endotoxin-treated polymorphonuclear leukocytes vehicle-treated control [umbilical cord blood polymorphonuclear leukocytes immune challenge cell culture] Davidson et al. compared the gene expression profiles of endotoxin-stimulated neonatal polymorphonuclear leukocytes (PMNs) and monocytes (MONOs) to elucidate inflammatory control mechanisms in the newborns. Umbilical cord blood was obtained from placentas immediately after term elective cesarean deliveries. PMNs and MONOs were separately isolated from the same blood sample and treated with 10 ng/ml LPS (endotoxin) or with PBS (vehicle) for 4 hours. 5 5 PMID:23326478
GEO:GPL570
GEO:GSE39840
ProteinAtlas - tissue: bone marrow bone marrow [tissue bone marrow] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE9159-3 myometrium term labor preterm in labor with inflammation [myometrium cesarean section failure to progress term labor inflammation spontaneous preterm labor preterm premature rupture of membranes preterm labor] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
ProteinAtlas - cell line: SH-SY5Y SH-SY5Y cell [cell line SH-SY5Y] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE18044-1 chorionic villus smoker non-smoker [placenta smoking] To determine the effects of tobacco smoke on the placental transcriptome, Bruchova et al. performed gene expression profiling in term placentas from women exposed to tobacco smoke in pregnancy and from those without significant exposure. Smoking status of the women was defined based on questionnaire data supported by cotinine plasma concentrations. Villus parenchymal sections were obtained by dissecting a 1.5 cm² segment approximately 5 cm from the cord insertion site and then splitting it into three equal parts: maternal (including the thin basal plate), middle, and fetal (including the chorionic plate). Total RNA was isolated from the middle section. 12 64 PMID:20053520
GEO:GPL6104
GEO:GSE18044
ProteinAtlas - cell line: A549 cell culture [cell line A549] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE39043-2 endometrium diestrus (day 8) estrus (day 0) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE5999[B]-8 decidua basal plate at 23–24 weeks basal plate at 21 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE5999|B5 decidua 21 weeks pregnant 18-19 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE9159|4 myometrium term labor term not in labor [myometrium cesarean section failure to progress term labor breech presentation] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE5999[A]-8 decidua basal plate at 23–24 weeks basal plate at 21 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE31976-3 umbilical cord blood non-Treg cells from maternal blood non-Treg cells from nonpregnant control [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE5999[B]-5 decidua basal plate at 21 weeks basal plate at 18–19 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE39043-1 endometrium early diestrus (day 3) estrus (day 0) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
ProteinAtlas - cell line: SCLC-21H cell culture [cell line SCLC-21H] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE25335-2 corpus luteum day 12 simulated early pregnancy day 10 simulated early pregnancy [corpus luteum simulated early pregnancy chorionic gonadotrophin drug treatment] To explore chorionic gonadotrophin (CG)-regulated gene expression in the primate corpus luteum (CL) during simulated early pregnancy (SEP), Bishop et al. treated female rhesus monkeys with increasing dosages of hCG mimicking the rise detected during early pregnancy. SEP treatment began on day 9 of the luteal phase. The first day of the luteal phase was defined as the first day of low serum E (<100 pg/ml) following the mid-cycle E surge, with a coincident rise in serum P above 0.2 ng/ml. Individual CL were collected on days 10, 12, 15, and 18 of the luteal phase, representing 1, 3, 6 and 9 days of hCG treatment. Additionally, CL were collected from untreated monkeys on day 10 of the luteal phase to serve as baseline controls. 4 4 PMID:22072816
GEO:GPL3535
GEO:GSE25335
GEO:GSE9159|1 myometrium preterm in labor with inflammation preterm not in labor and no inflammation [myometrium cesarean section inflammation spontaneous preterm labor preterm premature rupture of membranes preterm labor preeclampsia] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE31976-6 umbilical cord blood non-Treg cells from cord blood non-Treg cells from maternal blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 3 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE9159-4 myometrium term labor term not in labor [myometrium cesarean section failure to progress term labor breech presentation] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE56899-2 blood plasma second trimester pregnancy non-pregnant control [maternal plasma normal pregnancy second trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
ProteinAtlas - cell line: Hep G2 Hep-G2 cell [cell line Hep G2] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE48424-1 blood non-severe preeclampsia normal pregnancy [maternal blood preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia. The study included 13 women with severe preeclampsia, 6 women with non-severe preeclampsia, and 19 women with normal pregnancies. The criteria used to define severe preeclampsia included one of the following conditions: blood pressure higher than 160/110 mmHg, proteinuria higher than 1500 mg/24 h, maternal cerebral symptoms (seizures, stroke), intrauterine growth restriction below the 3° percentile, or multisystem disorder. Blood samples were collected from participants at the time of study inclusion. 5 18 PMID:24349325
GEO:GPL6480
GEO:GSE48424
GEO:GSE5809-1 endometrial stroma TCM-treated human endometrial stromal cells at 3 hours CCM-treated human endometrial stromal cells at 3 hours [endometrial stromal cells decidualization cell culture] To investigate paracrine communications that occur at the decidua-trophoblast interface, Hess et al. studied the effects of products secreted from human trophoblasts on global gene expression in in vitro-decidualized human endometrial stromal cells. Human endometrial stromal cells were decidualized with progesterone and cultured in human trophoblast-conditioned media (TCM), or in conditioned media from non-decidualized stromal cells (CCM) as a control. 3 3 PMID:17021345
GEO:GPL570
GEO:GSE5809
GEO:GSE5999[B]-10 decidua basal plate at 37–40 weeks basal plate at 23–24 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE25906-1 placenta preeclamptic pregnancy normal pregnancy [placenta preeclampsia] Tsai et al. conducted microarray profiling on a large set of human placentas (23 preeclamptic, 37 control) in order to uncover gene expression patterns associated with preeclampsia. Women were diagnosed with preeclampsia if their systolic blood pressure was at least 140 mm Hg, their diastolic blood pressure was at least 90 mm Hg, and they had proteinuria with an estimated 300 mg of protein or greater excreted in 24 hours measured directly or indirectly by protein creatinine ratio. Placental samples approximately 2 cm³ in size were dissected within 5 cm of the umbilical insertion site. 23 37 PMID:21183218
GEO:GPL6102
GEO:GSE25906
GEO:GSE31976-2 umbilical cord blood Treg cells from maternal blood Treg cells from nonpregnant control [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 5 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
ProteinAtlas - tissue: salivary gland saliva-secreting gland [tissue salivary gland] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE46510|5 blood preterm birth at >7 days and <37 weeks preterm birth after 48 hours and within 7 days [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 15 12 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE5999|A7 decidua 37-40 weeks pregnant 18-19 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE31329-1 myometrium myometrium under high tension myometrium under low tension [myometrium tissue culture] Tattersall et al. aimed to identify factors that mediate the effect of stretch on human myometrium. The study obtained myometrial samples from non-laboring patients, undergoing routine elective cesarean section at 38-40 weeks of pregnancy, for microarray analysis. Human myometrial explants were maintained in prolonged culture (65 hours) under either low tension (0.6 g) or high tension (2.4 g). Following culture, the samples were trimmed to remove tissue that had not been incubated under tension, snap frozen in liquid nitrogen, and stored at −80 °C. 9 9 PMID:22411014
GEO:GPL6883
GEO:GSE31329
ProteinAtlas - tissue: colon colon [tissue colon] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: skin skin of body [tissue skin] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE56899|2 blood plasma second trimester pregnancy non-pregnant control [maternal plasma normal pregnancy second trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE18162-1 placenta ethanol consumption no ethanol consumption [placenta fetal alcohol syndrome drinking] Rosenberg et al. conducted a preliminary investigation to determine whether ethanol-induced alterations in placental gene expression may have some utility as a diagnostic indicator of maternal drinking during pregnancy and as a prognostic indicator of risk for adverse neurobehavioral outcomes in affected offspring. Pregnant Long-Evans rats voluntarily consumed either a 0% or 5% ethanol solution 4 hours each day throughout gestation. Placentas were harvested on gestational day 20 for gene expression studies. 4 3 PMID:20053520
GEO:GPL1355
GEO:GSE18162
GEO:GSE9159-2 myometrium term not in labor preterm not in labor and no inflammation [myometrium cesarean section breech presentation preeclampsia] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE64884-1 blood third trimester pregnancy first trimester pregnancy [maternal blood natural killer cells normal pregnancy third trimester first trimester gestational age] To predict the role of microRNAs within gene regulatory networks of maternal peripheral blood natural killer (pNK) cells during pregnancy, Ishida et al. performed comprehensive miRNA and gene expression profiling of maternal pNK cells using a combination of real-time PCR-based array and DNA microarray analyses. Samples were obtained from the same healthy pregnant females during the first (7–11 weeks) and third trimesters (36–38 weeks) of gestation. 5 5 PMID:25824636
GEO:GPL13497
GEO:GSE64884
ProteinAtlas - cell line: MOLT-4 MOLT-4 cell [cell line MOLT-4] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE9984-1 chorionic villus second trimester pregnancy first trimester pregnancy [placenta normal pregnancy elective termination second trimester first trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45–59 days) and second trimester (109–115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the terminations or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
ProteinAtlas - cell line: HL-60 HL-60 cell [cell line HL-60] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE28551|1 placenta third trimester pregnancy first trimester pregnancy [placenta normal pregnancy third trimester elective termination first trimester gestational age] Sitras et al. investigated the differences in global gene expression profile between first and third trimester normal human placentas. Placental samples were collected from 21 women with uncomplicated pregnancies delivered at term and 16 healthy women undergoing termination of pregnancy at 9–12 weeks gestation. All women were healthy, Caucasian, and had low risk pregnancies. Chorionic tissue was dissected approximately 2 cm beside the umbilical cord insertion site, from the middle layer of placenta midway between maternal and fetal surfaces. 21 16 PMID:22442682
GEO:GPL2986
GEO:GSE28551
ProteinAtlas - cell line: MCF7 MCF-7 cell [cell line MCF7] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: kidney kidney [tissue kidney] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE40182|1 cytotrophoblast preeclampsia cytotrophoblasts at 0 hours preterm labor cytotrophoblasts at 0 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE53669-5 umbilical cord blood postpartum maternal plasma antepartum maternal plasma [maternal plasma normal pregnancy antepartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 3 3 PMID:17885688
GEO:GPL96
GEO:GSE53669
GEO:GSE31976|6 umbilical cord blood non-Treg cells from cord blood non-Treg cells from maternal blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 3 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE39290|1 placenta 930 mg/day choline supplement 480 mg/day choline supplement [placenta normal pregnancy third trimester choline drug treatment] Jiang et al. investigated the effects of maternal choline intake on the placental transcriptome, with a special interest in its role in modulating placental vascular function. Healthy third-trimester singleton pregnant women were randomized to choline intake groups of either 480 mg/day or 930 mg/day for 12 weeks. Placental samples were processed at the hospital within 90 minutes of delivery. After removal of the amnion, the placenta was visually divided into 4 quadrants, and full-thickness biopsies were taken from each quadrant. 6 6 PMID:23195033
GEO:GPL6480
GEO:GSE39290
ProteinAtlas - cell line: K-562 K-562 cell [cell line K-562] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: ovary female gonad [tissue ovary] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999[B]-1 decidua basal plate at 18–19 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE58435-1 amniotic fluid Turner syndrome fetus normal euploid fetus [amniotic fluid amniocentesis second trimester Turner syndrome genetic disorder] Massingham et al. utilized global gene expression analysis to interrogate the cell-free mRNA transcriptome from amniotic fluid supernatants of fetuses with Turner syndrome to understand pathophysiologic changes that are already present during the second trimester of gestation. Amniotic fluid supernatant samples were collected from women undergoing genetic testing for routine clinical indications at 15–18 weeks of gestation. 5 5 PMID:24850140
GEO:GPL570
GEO:GSE58435
GEO:GSE55439|1 placenta third trimester pregnancy first trimester pregnancy [placenta normal pregnancy cesarean section third trimester elective termination first trimester gestational age] To determine the acceptable timeframe for placental collection, Wolfe et al. collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to commercial solutions designed to preserve RNA (RNAlater™, Ambion) and DNA (DNAgard®, Biomatrica). First trimester (10-12 weeks) and third trimester (38-40 weeks) placental samples were collected from women undergoing abortion procedures and women undergoing scheduled term cesarean sections, respectively. Samples approximately 1 cm³ in size were obtained from the placental disc, halfway between the umbilical cord insertion point and the placental margin. Care was taken to exclude large blood vessels. Note: Only samples collected at 0 minutes in RNAlater™ were used for this analysis 9 9 PMID:24951174
GEO:GPL10558
GEO:GSE55439
ProteinAtlas - cell line: RH-30 Rh-30 cell [cell line RH-30] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE6909|1 placenta ADRA2B−/− genotype ADRA2B+/+ genotype [placenta gene knockout] Deletion of the 3 α2-adrenoceptor subtypes in the mouse results in embryonic lethality associated with a severe defect in the development of the extraembryonic vasculature and reduced activity of the ERK1/2 mitogen-activated protein kinases in the placenta and yolk sac at embryonic day 10.5. To search for antiangiogenic or angiogenic genes that might be dysregulated in the placentae of ADRA2B−/− embryos, Muthig et al. performed microarray expression profiling using RNA isolated from total placentae of E10.5 wild-type and mutant embryos with the maternal ADRA2B+/− genotype. 3 3 PMID:17673674
GEO:GPL1261
GEO:GSE6909
GEO:GSE5809|1 trophoblast trophoblast-conditioned medium for 3 hours control medium for 3 hours [trophoblasts endometrial stromal cells decidualization cell culture] To investigate paracrine communications that occur at the decidua-trophoblast interface, Hess et al. studied the effects of products secreted from human trophoblasts on global gene expression in in vitro-decidualized human endometrial stromal cells. Human endometrial stromal cells were decidualized with progesterone and treated with conditioned media from either human trophoblasts or non-decidualized stromal cells (control) for 0, 3, and 12 hours. 3 3 PMID:17021345
GEO:GPL570
GEO:GSE5809
GEO:GSE14771|B1 blood third trimester pregnancy non-pregnant female [maternal blood normal pregnancy third trimester gestational age] Heung et al. investigated the detection of fetal mRNA in maternal whole blood to determine if it offered advantages over maternal plasma analysis. Peripheral blood samples were collected from 5 third-trimester healthy women with singleton uncomplicated pregnancies (38–39 weeks) and 5 age-matched healthy non-pregnant females. 5 5 PMID:19516908
GEO:GPL97
GEO:GSE14771
GEO:GSE10392|1 uterine cervix medroxyprogesterone acetate treatment vehicle treatment [uterine cervix progesterone cervical ripening drug treatment] Xu et al. sought to assess novel pathways by which progestational agents (PAs) may modify signal transduction pathways that are involved in cervical ripening. For microarray analysis, pregnant CD-1 dams were randomized to subcutaneous injection with either medroxyprogesterone acetate (1 mg/dam) or EtOH (vehicle) at embryonic day 15. Cervical tissues from each treatment group were harvested 48 hours after injection. 6 6 PMID:18313454
GEO:GPL1261
GEO:GSE10392
ProteinAtlas - cell line: SK-MEL-30 SK-MEL-30 cell [cell line SK-MEL-30] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE48424|1 blood non-severe preeclampsia normal pregnancy [maternal blood severe preeclampsia preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia (PE). The study included 13 women with severe PE, 6 women with non-severe PE, and 19 women with normal pregnancies. The diagnosis of PE was based on changes in blood pressure, proteinuria and increased uricemia. 5 18 PMID:24349325
GEO:GPL6480
GEO:GSE48424
GEO:GSE31976-4 umbilical cord blood non-Treg cells from maternal blood Treg cells from maternal blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 5 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE5999|B3 decidua 23-24 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
ProteinAtlas - tissue: esophagus esophagus [tissue esophagus] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: NTERA-2 NTERA-2 cell [cell line NTERA-2] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE53669-4 umbilical cord blood umbilical cord plasma antepartum maternal plasma [umbilical cord plasma maternal plasma maternal blood normal pregnancy antepartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 3 3 PMID:17885688
GEO:GPL96
GEO:GSE53669
GEO:GSE5999[B]-7 decidua basal plate at 37–40 weeks basal plate at 18–19 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE40182-1 cytotrophoblast preeclampsia cytotrophoblasts at 0 hours preterm labor cytotrophoblasts at 0 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 5 5 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE7586|2 chorionic villus chronic placental malaria (inflammation) uninfected control (no inflammation) [placenta inflammation infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 7 9 PMID:17579077
GEO:GPL570
GEO:GSE7586
GEO:GSE5999[A]-9 decidua basal plate at 37–40 weeks basal plate at 21 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - tissue: cerebral cortex cerebral cortex [tissue cerebral cortex] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE48424|3 blood severe preeclampsia non-severe preeclampsia [maternal blood severe preeclampsia preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia (PE). The study included 13 women with severe PE, 6 women with non-severe PE, and 19 women with normal pregnancies. The diagnosis of PE was based on changes in blood pressure, proteinuria and increased uricemia. 12 5 PMID:24349325
GEO:GPL6480
GEO:GSE48424
GEO:GSE30915-3 trophoblast BMP4-treated human embryonic stem cells at day 6 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE5999[A]-2 decidua basal plate at 21 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE31976|2 blood Treg cells from maternal blood Treg cells from non-pregnant control [maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 5 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE14722[A]-1 decidua basal plate from preeclamptic pregnancy gestational age-matched control [basal plate spontaneous preterm birth preterm labor preeclampsia] Winn et al. conducted a global analysis of gene expression at the maternal-fetal interface in placental samples from women with preeclampsia versus samples from women who delivered due to preterm labor with no evidence of infection. The basal plate was dissected from the placenta proper and diced into approximately 3 mmᶾ pieces for RNA extraction. Pregnancies complicated by multiple gestations, fetal anomalies, premature rupture of the membranes, infection, diabetes, or other autoimmune diseases were excluded from the study. 12 11 PMID:18818296
GEO:GPL96
GEO:GSE14722
GEO:GSE40182-4 cytotrophoblast preeclampsia cytotrophoblasts at 48 hours preterm labor cytotrophoblasts at 48 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 4 4 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE5999|B2 decidua 21 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE12767|1 chorionic villus first trimester CVS from preeclamptic pregnancy first trimester CVS from normal pregnancy [chorionic villus chorionic villus sampling first trimester preeclampsia] Founds et al. performed global gene expression profiling in first trimester placentas of women who later manifested preeclampsia to better seek clues to etiology and early circulating biomarkers of placental origin. Surplus chorionic villus sampling (CVS) tissues were collected at 10-12 weeks gestation in 160 patients with singleton fetuses. Four patients developed preeclampsia, and their banked CVS specimens were matched to 8 control samples from patients with unaffected pregnancies. As part of the routine CVS procedure, if surplus tissue not needed for clinical analyses was available, villi grossly free of decidua and maternal blood were removed from solution in the Petri dish and snap-frozen for microarray analysis. 4 8 PMID:19027158
GEO:GPL570
GEO:GSE12767
ProteinAtlas - tissue: heart muscle myocardium [tissue heart muscle] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: placenta placenta [tissue placenta] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE38095-1 placenta 50% food restriction ad libitum fed [placenta maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed, 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two placentas from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
ProteinAtlas - cell line: HEK 293 HEK-293 cell [cell line HEK 293] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999[A]-1 decidua basal plate at 18–19 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE56899|1 blood plasma first trimester pregnancy non-pregnant control [maternal plasma normal pregnancy first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE10392-1 uterine cervix medroxyprogesterone acetate-treated female vehicle-treated control [uterine cervix progesterone cervical ripening drug treatment] Xu et al. sought to assess novel pathways by which progestational agents may modify signal transduction pathways that are involved in cervical ripening. For microarray analysis, pregnant CD-1 dams were randomized to subcutaneous injection with either medroxyprogesterone acetate or EtOH (vehicle) at embryonic day 15. Cervical tissues from each treatment group were harvested 48 hours after injection. 6 6 PMID:18313454
GEO:GPL1261
GEO:GSE10392
GEO:GSE25335-4 corpus luteum day 18 simulated early pregnancy day 15 simulated early pregnancy [corpus luteum simulated early pregnancy chorionic gonadotrophin drug treatment] To explore chorionic gonadotrophin (CG)-regulated gene expression in the primate corpus luteum (CL) during simulated early pregnancy (SEP), Bishop et al. treated female rhesus monkeys with increasing dosages of hCG mimicking the rise detected during early pregnancy. SEP treatment began on day 9 of the luteal phase. The first day of the luteal phase was defined as the first day of low serum E (<100 pg/ml) following the mid-cycle E surge, with a coincident rise in serum P above 0.2 ng/ml. Individual CL were collected on days 10, 12, 15, and 18 of the luteal phase, representing 1, 3, 6 and 9 days of hCG treatment. Additionally, CL were collected from untreated monkeys on day 10 of the luteal phase to serve as baseline controls. 4 4 PMID:22072816
GEO:GPL3535
GEO:GSE25335
GEO:GSE46510-2 blood preterm birth after 48 hours and within 7 days spontaneous preterm birth within 48 hours [maternal blood preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 12 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
ProteinAtlas - cell line: HMC-1 HMC-1 cell [cell line HMC-1] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE28277-1 placenta diabetic pregnancy normal pregnancy [placenta gestational diabetes diabetes] Using a mouse model of diabetic pregnancy, Salbaum et al. assayed placental gene expression in diabetic placentas to investigate cellular and molecular alterations linked to compromised placental function in gestational diabetes. Diabetes was induced in 7- to 9-week-old FVB female mice by two intraperitoneal injections of streptozotocin. Placentas were dissected from FVB dams under diabetic conditions and untreated controls at embryonic day 10.5. 5 5 PMID:21491160
GEO:GPL1261
GEO:GSE28277
ProteinAtlas - tissue: thyroid gland thyroid gland [tissue thyroid gland] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE46510-3 blood preterm birth after 7 days spontaneous preterm birth within 48 hours [maternal blood preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 15 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE38095|2 placenta 50% food restriction with leptin replacement ad libitum fed [placenta leptin maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed (control), 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
ProteinAtlas - tissue: lung lung [tissue lung] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: fallopian tube fallopian tube [tissue fallopian tube] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: U-266/84 U-266 cell [cell line U-266/84] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE56899|4 blood plasma postpartum non-pregnant control [maternal plasma normal pregnancy postpartum gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE22490-1 placenta recurrent miscarriage first trimester pregnancy [placenta elective termination first trimester recurrent miscarriage] Rull et al. aimed to profile whole-genome differential gene expression in the first trimester placental tissue in cases of recurrent miscarriage (RM) compared to gestational age-matched uncomplicated pregnancies. Placental tissue samples were obtained during elective surgical abortion of uncomplicated pregnancy or uterine curettage due to recurrent incomplete or delayed miscarriage. The recruited RM patients had experienced at least three consecutive miscarriage events. 4 6 PMID:23290504
GEO:GPL570
GEO:GSE22490
ProteinAtlas - tissue: endometrium endometrium [tissue endometrium] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: tonsil tonsil [tissue tonsil] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE46510|1 blood no spontaneous preterm birth within 48 hours spontaneous preterm birth within 48 hours [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 106 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
ProteinAtlas - cell line: AN3-CA AN3CA cell [cell line AN3-CA] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: NB-4 NB-4 cell [cell line NB-4] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE38095-2 placenta 50% food restriction with leptin replacement ad libitum fed [placenta leptin maternal nutrition] Schulz et al. tested the hypothesis that some of the effects of maternal food restriction on placental development are mediated by loss of leptin. Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: ad libitum fed, 50% food restriction, or 50% food restriction with leptin replacement. Placentas were collected on day 11.5, and two placentas from each mother were pooled for microarray analysis. 5 5 PMID:22993381
GEO:GPL11202
GEO:GSE38095
GEO:GSE5999|B4 decidua 37-40 weeks pregnant 14-16 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE25903-1 decidua pseudopregnant (deciduoma) pregnant (decidua) [decidua decidualization implantation] McConaha et al. compared the gene expression profile of the developing decidua in pregnant mice with the deciduoma formed after artificial induction in an effort to identify conceptus-influenced changes in uterine gene expression during decidualization. Decidualization was artificially induced by transferring blastocyst-sized ConA-coated agarose beads into the uterus on day 2.5 of pseudopregnancy. Total RNA was isolated for microarray analysis on day 7.5 from blastocyst and bead-induced 'implantation' sites of the uteri of pregnant (decidua) and pseudopregnant (deciduoma) mice, respectively. 3 3 PMID:21300692
GEO:GPL6481
GEO:GSE25903
GEO:GSE18850-1 placenta elective term cesarean section normal pregnancy [placenta cesarean section normal pregancy] To test the hypothesis that the labor process involves changes in mRNA expression in the placenta, Chim et al. interrogated the mRNA levels of >50,000 genes and transcript variants in placentas collected from term spontaneous delivery and elective term cesarean delivery by gene expression microarray. To minimize the effect of gestational age on gene expression, the two groups were matched for gestational age at delivery. A piece of placental tissue (about 0.1 cm³) was biopsied immediately after delivery. Care was taken to minimize the contamination of any maternal decidual tissue, fetal membranes, and blood clots in the biopsied placental tissue. 4 5 PMID:22496790
GEO:GPL570
GEO:GSE18850
GEO:GSE46286|1 amniotic fluid term pregnancy second trimester pregnancy [amniotic fluid normal pregnancy cesarean section third trimester amniocentesis second trimester gestational age] Hui et al. aimed to determine whether the relative representation of specific organs in term amniotic fluid cell-free fetal RNA would differ from that in second-trimester amniotic fluid. Using global gene expression analysis, the study compared 8 second-trimester amniotic fluid samples from routine amniocenteses to 8 term amniotic fluid samples from women undergoing prelabor cesarean deliveries. Amniotic fluid was collected at cesarean delivery after entry into the uterus and before rupture of the amniotic membranes. 8 8 PMID:23812459
GEO:GPL10558
GEO:GSE46286
GEO:GSE56899|3 blood plasma third trimester pregnancy non-pregnant control [maternal plasma normal pregnancy third trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE32178|1 myometrium dystocic labor normal labor [myometrium cesarean section spontaneous labor dystocia] Brennan et al. used gene expression microarrays to examine the temporal and spatial changes in myometrial gene expression during normally-progressing and dystocic labors to improve our understanding of the molecular mechanisms underlying term dystocic labor. Myometrial biopsies were obtained from the lower uterine segment in women undergoing cesarean section for dystocia and in control women undergoing cesarean section for persistent occiput posterior position. All patients were in spontaneous (non-induced) labor and had received intrapartum oxytocin to accelerate labor. 4 4 PMID:21999197
GEO:GPL570
GEO:GSE32178
GEO:GSE20499-1 endometrium endometrial natural killer cells decidual natural killer cells [endometrium decidua natural killer cells cell culture] Kopcow et al. compared human natural killer cells from the decidua basalis of gravid uteri and from cycling endometrium of women undergoing hysterectomy by gene expression profiling. Decidual natural killer cells were isolated from the decidua basalis of first trimester placentas and FACS sorted as CD3-, CD16-, CD56+ cells. Endometrial natural killer cells were obtained from non-affected regions of cycling endometrium of donor women undergoing hysterectomy and FACS sorted as CD45+, CD56+, CD3- cells. 5 4 PMID:20172608
GEO:GPL570
GEO:GSE20499
GEO:GSE28551-1 placenta third trimester pregnancy first trimester pregnancy [placenta normal pregnancy third trimester elective termination first trimester gestational age] Sitras et al. investigated the differences in global gene expression profile between first and third trimester normal human placentas. Placental samples were collected from 21 women with uncomplicated pregnancies delivered at term and 16 healthy women undergoing termination of pregnancy at 9–12 weeks of gestation. All women were healthy, Caucasian, and had low risk pregnancies. Chorionic tissue was dissected approximately 2 cm beside the umbilical cord insertion site, from the middle layer of placenta midway between maternal and fetal surfaces. 21 16 PMID:22442682
GEO:GPL2986
GEO:GSE28551
GEO:GSE30915-2 trophoblast BMP4-treated human embryonic stem cells at day 4 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE31976|1 blood non-Treg cells from non-pregnant control Treg cells from non-pregnant control [maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 4 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
ProteinAtlas - cell line: U-266/70 U-266 cell [cell line U-266/70] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE54618-1 placenta preeclamptic pregnancy normotensive pregnancy [placenta preeclampsia] To identify genes and pathways correlating with β-glucocerebrosidase (GBA) expression, Jebbink et al. performed microarray expression profiling on placental tissue from normotensive patients with low GBA expression and from preeclamptic patients with high GBA expression. Quantitative RT-PCR was used to determine normotensive and preeclamptic placentas with the most extreme levels of GBA expression prior to microarray analysis. Placental biopsies were obtained immediately after delivery from a macroscopically viable (non-infarcted) central cotyledon from the maternal side. 4 12 PMID:25552189
GEO:GPL10558
GEO:GSE54618
ProteinAtlas - tissue: lymph node lymph node [tissue lymph node] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE39043-3 endometrium late diestrus (day 12) estrus (day 0) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE31976-5 umbilical cord blood Treg cells from cord blood Treg cells from maternal blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 4 5 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE56899|6 blood plasma third trimester pregnancy first trimester pregnancy [maternal plasma normal pregnancy third trimester first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
ProteinAtlas - cell line: SK-BR-3 SK-BR-3 cell [cell line SK-BR-3] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE32178-1 myometrium dystocic labor normal labor [myometrium cesarean section spontaneous labor dystocia] Brennan et al. used microarray profiling to examine the temporal and spatial changes in myometrial gene expression during normally-progressing and dystocic labors to improve our understanding of the molecular mechanisms underlying term dystocic labor. Myometrial biopsies were obtained from the lower uterine segment in women undergoing cesarean section for dystocia and in control women undergoing cesarean section for persistent occiput posterior position. All patients were in spontaneous (non-induced) labor and had received intrapartum oxytocin to accelerate labor. 4 4 PMID:21999197
GEO:GPL570
GEO:GSE32178
GEO:GSE9773|1 cytotrophoblast first trimester extravillous trophoblasts first trimester villous cytotrophoblasts [cytotrophoblasts first trimester trophoblast invasion cell culture] To gain more insight into the regulatory mechanisms of trophoblast invasion, Bilban et al. investigated whole-genome gene expression profiles of nonmigratory villous cytotrophoblasts (CTBs) and invasive, extravillous trophoblasts (EVTs) purified from first trimester placentae and differentiating villous explant cultures, respectively. For microarray analysis, villous CTBs were purified from first trimester placentae and grown in culture for 24 hours, whereas EVTs were collected from first trimester villous explants seeded on Matrigel after 72 hours. 6 5 PMID:18845641
GEO:GPL96
GEO:GSE9773
GEO:GSE25861-1 chorionic villus intrauterine growth restriction gestational age-matched control [placental microvascular endothelial cells spontaneous preterm birth preterm labor preeclampsia intrauterine growth restriction cell culture] Dunk et al. investigated the differential gene expression profiles of placental microvascular endothelial cells (PlMECs) in pregnancies complicated by severe early-onset intrauterine growth restriction (IUGR) with or without superimposed preeclampsia versus gestational age-matched preterm controls. Severe IUGR preterm placentas were collected from patients with fetal weight ≤10th percentile with AREDV in the umbilical artery and being delivered for obstetrical indications at 24–34 weeks of gestation. Preterm control placentas were collected from preterm pregnancies with appropriately grown fetuses that were delivered following preterm labor at 24–34 weeks of gestation. Preterm placentas with chorioamnionitis were excluded. Placental tissue, taken from the distal (i.e. maternal) side of the placenta, was digested and PlMECs positively selected using tocosylated magnetic Dynabeads labeled with Human Endothelial Antigen lectin. 6 3 PMID:22264586
GEO:GPL570
GEO:GSE25861
GEO:GSE65265-2 uterine cervix pregnant cervix without Mφs nonpregant cervix without Mφs [uterine cervix tissue macrophages] To test the hypothesis that expression of genes unique to resident macrophages (Mφs) distinguishes the late remodeled prepartum from unremodeled nonpregnant cervix, Dobyns et al. performed a microarray analysis on perfused cervix, with or without Mφs, from prepartum day 21 postbreeding and nonpregnant rats. Cells from the cervix in the macrophage-depleted groups were subjected to a magnetic bead separation procedure to remove Mφs. 3 3 PMID:25811906
GEO:GPL14746
GEO:GSE65265
GEO:GSE9984|1 chorionic villus second trimester pregnancy first trimester pregnancy [placenta normal pregnancy elective termination second trimester first trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45-59 days) and second trimester (109-115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the termination or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
ProteinAtlas - cell line: A-431 A-431 cell [cell line A-431] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE31976-1 umbilical cord blood non-Treg cells from nonpregnant control Treg cells from nonpregnant control [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 4 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE39290-1 placenta 930 mg/day choline supplement 480 mg/day choline supplement [placenta normal pregnancy third trimester choline drug treatment] Jiang et al. investigated the effects of maternal choline intake on the placental transcriptome, with a special interest in its role in modulating placental vascular function. Healthy third-trimester singleton pregnant women were randomized to choline intake groups of either 480 mg/day or 930 mg/day for 12 weeks. Placental samples were processed at the hospital within 90 minutes of delivery. After removal of the amnion, the placenta was visually divided into four quadrants, and full-thickness biopsies were taken from each quadrant. 6 6 PMID:23195033
GEO:GPL6480
GEO:GSE39290
GEO:GSE46510|6 blood term delivery preterm birth after 48 hours and within 7 days [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 12 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE9159-1 myometrium preterm in labor with inflammation preterm not in labor and no inflammation [myometrium cesarean section inflammation spontaneous preterm labor preterm premature rupture of membranes preterm labor preeclampsia] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE39043-7 endometrium early estrus (day 16) early diestrus (day 3) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE27272-1 umbilical cord blood smoker non-smoker [maternal blood prenatal tobacco exposure smoking] Votavova et al. performed a comprehensive analysis of transcriptome alterations induced by smoking in maternal and fetal cells. Samples of peripheral blood, placenta, and cord blood were obtained from pregnant smokers and gravidas without significant exposure to tobacco smoke. Smoking status was confirmed by detection of excessive plasma levels of cotinine. Placental samples were prepared according to the protocol by Sood et al., as described in detail previously. 19 46 PMID:21803418
GEO:GPL6883
GEO:GSE27272
GEO:GSE53669-6 umbilical cord blood postpartum maternal plasma umbilical cord plasma [umbilical cord plasma maternal plasma normal pregnancy postpartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 3 3 PMID:17885688
GEO:GPL96
GEO:GSE53669
GEO:GSE6909-1 placenta Adra2b−/− placenta wild-type control [placenta gene knockout] Deletion of the 3 α2-adrenoceptor subtypes in the mouse results in embryonic lethality associated with a severe defect in the development of the extraembryonic vasculature and reduced activity of the ERK1/2 mitogen-activated protein kinases in the placenta and yolk sac. To search for antiangiogenic or angiogenic genes that might be dysregulated in the placentas of Adra2b−/− embryos, Muthig et al. performed whole genome expression profiling on wild-type and mutant placentas from pregnant Adra2b+/− mice. Placentas were harvested at embryonic day 10.5 for microarray analysis. 3 3 PMID:17673674
GEO:GPL1261
GEO:GSE6909
GEO:GSE14771[A]-1 blood third trimester pregnancy non-pregnant control [maternal blood normal pregnancy third trimester gestational age] Heung et al. investigated fetal mRNA detection in maternal whole blood and determined if it offered advantages over maternal plasma analysis. Peripheral whole blood samples were collected from third trimester healthy women with singleton uncomplicated pregnancies (38–39 weeks) and age-matched healthy non-pregnant females. 5 5 PMID:19516908
GEO:GPL96
GEO:GSE14771
GEO:GSE48424-2 blood severe preeclampsia normal pregnancy [maternal blood severe preeclampsia preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia. The study included 13 women with severe preeclampsia, 6 women with non-severe preeclampsia, and 19 women with normal pregnancies. The criteria used to define severe preeclampsia included one of the following conditions: blood pressure higher than 160/110 mmHg, proteinuria higher than 1500 mg/24 h, maternal cerebral symptoms (seizures, stroke), intrauterine growth restriction below the 3° percentile, or multisystem disorder. Blood samples were collected from participants at the time of study inclusion. 12 18 PMID:24349325
GEO:GPL6480
GEO:GSE48424
GEO:GSE7676|1 placenta PCDH12−/− genotype PCDH12+/+ genotype [placenta gene knockout] Protocadherin-12 (PCDH12) is expressed in angiogenic endothelial cells, mesangial cells of kidney glomeruli, and glycogen cells of the mouse placenta. To gain insight into the role of PCDH12 in vivo, Rampon et al. produced PCDH12-deficient mice and examined the gene expression profiles of knockout placentas compared with wild-type placentas at embryonic day 12.5. 5 5 PMID:18477666
GEO:GPL1261
GEO:GSE7676
GEO:GSE5999[A]-4 decidua basal plate at 37–40 weeks basal plate at 14–16 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE12767-1 chorionic villus first trimester CVS from preeclamptic pregnancy first trimester CVS from normal pregnancy [chorionic villus chorionic villus sampling first trimester preeclampsia] Founds et al. performed global gene expression profiling in first trimester placentas of women who later manifested preeclampsia to better seek clues to etiology and early circulating biomarkers of placental origin. Surplus chorionic villus sampling (CVS) tissues were collected at 10–12 weeks of gestation in 160 patients with singleton fetuses. Four patients developed preeclampsia, and their banked CVS specimens were matched to 8 control samples from patients with unaffected pregnancies. As part of the routine CVS procedure, if surplus tissue not needed for clinical analyses was available, villi grossly free of decidua and maternal blood were removed from solution in the Petri dish and snap frozen for microarray analysis. 4 8 PMID:19027158
GEO:GPL570
GEO:GSE12767
GEO:GSE27272-3 umbilical cord blood smoker non-smoker [umbilical cord blood prenatal tobacco exposure smoking] Votavova et al. performed a comprehensive analysis of transcriptome alterations induced by smoking in maternal and fetal cells. Samples of peripheral blood, placenta, and cord blood were obtained from pregnant smokers and gravidas without significant exposure to tobacco smoke. Smoking status was confirmed by detection of excessive plasma levels of cotinine. Placental samples were prepared according to the protocol by Sood et al., as described in detail previously. 19 45 PMID:21803418
GEO:GPL6883
GEO:GSE27272
GEO:GSE5809|2 trophoblast trophoblast-conditioned medium for 12 hours control medium for 12 hours [trophoblasts endometrial stromal cells decidualization cell culture] To investigate paracrine communications that occur at the decidua-trophoblast interface, Hess et al. studied the effects of products secreted from human trophoblasts on global gene expression in in vitro-decidualized human endometrial stromal cells. Human endometrial stromal cells were decidualized with progesterone and treated with conditioned media from either human trophoblasts or non-decidualized stromal cells (control) for 0, 3, and 12 hours. 2 3 PMID:17021345
GEO:GPL570
GEO:GSE5809
ProteinAtlas - tissue: testis testis [tissue testis] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE26315-2 amnion interleukin-1β challenge for 8 hours untreated control [amnion inflammation immune challenge cell culture] Using monolayer cultures of human amnion mesenchymal cells as a model, Li et al. aimed to detail the global programme of gene expression that occurs in response to cytokine challenge. Primary cultures of human amnion mesenchymal cells were prepared from amnion membranes obtained prior to labor at term and challenged with 10 ng/ml interleukin-1β for 1 hour or 8 hours in serum-free media, while control cells were treated with serum-free medium only. 3 3 PMID:21655103
GEO:GPL571
GEO:GSE26315
ProteinAtlas - tissue: spleen spleen [tissue spleen] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE56899|5 blood plasma second trimester pregnancy first trimester pregnancy [maternal plasma normal pregnancy second trimester first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE56899-5 blood plasma second trimester pregnancy first trimester pregnancy [maternal plasma normal pregnancy second trimester first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE5999[A]-10 decidua basal plate at 37–40 weeks basal plate at 23–24 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE5999[B]-4 decidua basal plate at 37–40 weeks basal plate at 14–16 weeks [basal plate normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE36083-1 placenta antiphospholipid antibody treatment untreated control [placenta antiphospholipid antibodies immune challenge tissue culture] Pantham et al. investigated the molecular changes that occur in placental explants upon treatment with antiphospholipid antibodies (aPL) in order to begin to understand how these antibodies change trophoblast death. Three first-trimester placentas (8–8.5 weeks) were obtained following elective termination of pregnancies, dissected into explants, and cultured with either 25 μg/ml aPL or untreated media for 16 hours. Microarray analysis was subsequently performed using RNA extracted from the cultured explants. 3 3 PMID:22542907
GEO:GPL570
GEO:GSE36083
GEO:GSE63901|2 endometrium elevated cyclin E levels normal cyclin E levels [endometrium progesterone drug treatment recurrent miscarriage recurrent early pregnancy loss] Kosova et al. characterized gene expression profiles of midsecretory endometria from women with recurrent early pregnancy loss. The study included 32 women of European ancestry with two or more documented unexplained miscarriages, who were classified into three groups based on endometrial histological dating and cyclin E levels. Abnormal endometrial histologies and abnormal cyclin E levels were defined as ≥3 days of endometrial developmental delay and >20% expression in the endometrial glandular cells, respectively. All women had endometrial biopsies performed during their mid-luteal phase, 9-11 days following the endogenous LH surge. For 5 additional women with elevated cyclin E levels, biopsy samples were collected in the mid-luteal phase both prior to and post-progesterone treatment to investigate the gene expression profiles in response to treatment. 18 46 PMID:25586782
GEO:GPL10558
GEO:GSE63901
ProteinAtlas - tissue: adrenal gland adrenal gland [tissue adrenal gland] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE56899|7 blood plasma third trimester pregnancy second trimester pregnancy [maternal plasma normal pregnancy third trimester second trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from four non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE5999|A5 decidua 21 weeks pregnant 18-19 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE25335-3 corpus luteum day 15 simulated early pregnancy day 12 simulated early pregnancy [corpus luteum simulated early pregnancy chorionic gonadotrophin drug treatment] To explore chorionic gonadotrophin (CG)-regulated gene expression in the primate corpus luteum (CL) during simulated early pregnancy (SEP), Bishop et al. treated female rhesus monkeys with increasing dosages of hCG mimicking the rise detected during early pregnancy. SEP treatment began on day 9 of the luteal phase. The first day of the luteal phase was defined as the first day of low serum E (<100 pg/ml) following the mid-cycle E surge, with a coincident rise in serum P above 0.2 ng/ml. Individual CL were collected on days 10, 12, 15, and 18 of the luteal phase, representing 1, 3, 6 and 9 days of hCG treatment. Additionally, CL were collected from untreated monkeys on day 10 of the luteal phase to serve as baseline controls. 4 4 PMID:22072816
GEO:GPL3535
GEO:GSE25335
GEO:GSE5999[B]-3 decidua basal plate at 23–24 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE46510|4 blood term delivery spontaneous preterm birth within 48 hours [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE54618-2 placenta preeclamptic + HELLP pregnancy normotensive pregnancy [placenta HELLP syndrome preeclampsia] To identify genes and pathways correlating with β-glucocerebrosidase (GBA) expression, Jebbink et al. performed microarray expression profiling on placental tissue from normotensive patients with low GBA expression and from preeclamptic patients with high GBA expression. Quantitative RT-PCR was used to determine normotensive and preeclamptic placentas with the most extreme levels of GBA expression prior to microarray analysis. Placental biopsies were obtained immediately after delivery from a macroscopically viable (non-infarcted) central cotyledon from the maternal side. 7 12 PMID:25552189
GEO:GPL10558
GEO:GSE54618
GEO:GSE39043-8 endometrium late diestrus (day 12) diestrus (day 8) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE31976|7 umbilical cord blood non-Treg cells from cord blood Treg cells from cord blood [cord blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 3 4 PMID:23733877
GEO:GPL6947
GEO:GSE31976
GEO:GSE39043-10 endometrium early estrus (day 16) late diestrus (day 12) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
ProteinAtlas - cell line: U-138 MG U-138MG cell [cell line U-138 MG] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999|A6 decidua 23-24 weeks pregnant 18-19 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - cell line: THP-1 THP-1 cell [cell line THP-1] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE43942-1 placenta preeclamptic pregnancy normal pregnancy [placenta preeclampsia] Xiang et al. performed global gene expression profiling of placental tissue from preeclamptic pregnancies and uncomplicated pregnancies to explore genes with differential expression. Placentas from normal and preeclamptic pregnancies were collected immediately after cesarean section, and two 1 cmᶾ fragments were dissected for microarray analysis. 5 7 PMID:23544093
GEO:GPL10191
GEO:GSE43942
GEO:GSE24129|1 chorionic villus preeclamptic pregnancy normal pregnancy [placenta cesarean section preeclampsia] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
ProteinAtlas - cell line: PC-3 PC-3 cell [cell line PC-3] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE14771[B]-1 blood third trimester pregnancy non-pregnant control [maternal blood normal pregnancy third trimester gestational age] Heung et al. investigated fetal mRNA detection in maternal whole blood and determined if it offered advantages over maternal plasma analysis. Peripheral whole blood samples were collected from third trimester healthy women with singleton uncomplicated pregnancies (38–39 weeks) and age-matched healthy non-pregnant females. 5 5 PMID:19516908
GEO:GPL97
GEO:GSE14771
ProteinAtlas - cell line: CAPAN-2 CAPAN-2 cell [cell line CAPAN-2] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE46286-1 amniotic fluid third trimester pregnancy second trimester pregnancy [amniotic fluid normal pregnancy cesarean section third trimester amniocentesis second trimester gestational age] Hui et al. investigated whether the relative representation of organ-specific transcripts in amniotic fluid cell-free fetal RNA differs between second trimester and term pregnancies. Microarray analysis was performed on amniotic fluid samples from women who underwent routine amniocenteses at 16–19 weeks of gestation and from women undergoing scheduled prelabor cesarean deliveries at 37–40 weeks of gestation. 8 8 PMID:23812459
GEO:GPL10558
GEO:GSE46286
GEO:GSE55439-1 placenta third trimester pregnancy first trimester pregnancy [placenta normal pregnancy cesarean section third trimester elective termination first trimester gestational age] To determine the acceptable timeframe for placental collection, Wolfe et al. collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to commercial solutions designed to preserve RNA and DNA. First trimester (10–12 weeks) and third trimester (38–40 weeks) placental samples were collected from women undergoing abortion procedures and women undergoing scheduled term cesarean sections, respectively. Samples approximately 1 cm³ in size were obtained from the placental disc, halfway between the umbilical cord insertion point and the placental margin. Note: Only samples collected at 0 minutes in RNAlater™ were used for this analysis 9 9 PMID:24951174
GEO:GPL10558
GEO:GSE55439
ProteinAtlas - cell line: RPMI-8226 RPMI-8226 cell [cell line RPMI-8226] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE14722|A1 decidua preeclampsia basal plate biopsy preterm basal plate biopsy [basal plate preterm labor preeclampsia] Winn et al. conducted a global analysis of gene expression at the maternal-fetal interface in placental samples from women with preeclampsia versus samples from women who delivered due to preterm labor with no evidence of infection. The basal plate was dissected from the placenta proper and diced into approximately 3 mmᶾ pieces, which were snap frozen in liquid nitrogen and stored at −70 °C. Pregnancies complicated by multiple gestations, fetal anomalies, premature rupture of the membranes, infection, diabetes, or other autoimmune diseases were excluded. 12 11 PMID:18818296
GEO:GPL96
GEO:GSE14722
GEO:GSE5999|A4 decidua 37-40 weeks pregnant 14-16 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE5999[A]-3 decidua basal plate at 23–24 weeks basal plate at 14–16 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - cell line: EFO-21 cell culture [cell line EFO-21] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE39043-5 endometrium diestrus (day 8) early diestrus (day 3) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE5999|B6 decidua 23-24 weeks pregnant 18-19 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
ProteinAtlas - cell line: BEWO BeWo cell [cell line BEWO] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: stomach stomach [tissue stomach] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE31976|5 umbilical cord blood Treg cells from cord blood Treg cells from maternal blood [cord blood maternal blood immune tolerance cellular immunity regulatory T cells] Santner-Nanan et al. searched for evidence of transplacental programming in cellular immunity by characterizing the gene expression profiles in maternal and fetal regulatory T (Treg) cells. Peripheral blood samples from pregnant women were taken 2-5 hours before delivery, and cord blood was obtained at delivery. Treg cells and non-Treg cells were sorted by Ficoll-Hypaque gradient centrifugation, and total RNA was extracted for microarray analysis. 4 5 PMID:23733877
GEO:GPL6947
GEO:GSE31976
ProteinAtlas - tissue: urinary bladder urinary bladder [tissue urinary bladder] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE9984-2 chorionic villus third trimester pregnancy first trimester pregnancy [placenta normal pregnancy cesarean section third trimester elective termination first trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45–59 days) and second trimester (109–115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the terminations or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
GEO:GSE14722[B]-1 decidua basal plate from preeclamptic pregnancy gestational age-matched control [basal plate spontaneous preterm birth preterm labor preeclampsia] Winn et al. conducted a global analysis of gene expression at the maternal-fetal interface in placental samples from women with preeclampsia versus samples from women who delivered due to preterm labor with no evidence of infection. The basal plate was dissected from the placenta proper and diced into approximately 3 mmᶾ pieces for RNA extraction. Pregnancies complicated by multiple gestations, fetal anomalies, premature rupture of the membranes, infection, diabetes, or other autoimmune diseases were excluded from the study. 12 11 PMID:18818296
GEO:GPL97
GEO:GSE14722
ProteinAtlas - cell line: WM-115 WM-115 cell [cell line WM-115] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE24129|2 chorionic villus fetal growth restriction normal pregnancy [placenta cesarean section fetal growth restriction] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
GEO:GSE5999|A3 decidua 23-24 weeks pregnant 14-16 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - cell line: Karpas-707 cell culture [cell line Karpas-707] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: prostate prostate gland [tissue prostate] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999[A]-5 decidua basal plate at 21 weeks basal plate at 18–19 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL96
GEO:GSE5999
GEO:GSE39043-9 endometrium early estrus (day 16) diestrus (day 8) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE10588-1 placenta severe preeclampsia normal pregnancy [placenta severe preeclampsia preeclampsia] Sitras et al. investigated the global placental gene expression profile in severe preeclampsia. Twenty-one women were randomly selected from 50 participants with uncomplicated pregnancies to match 21 patients with severe preeclampsia. Five preeclamptic placentas were excluded because of poor RNA quality, leaving 16 preeclamptic placentas for microarray experiments. Chorionic tissue was dissected from the middle layer of placenta midway between maternal and fetal surfaces, approximately 2 cm beside the umbilical cord insertion. 17 26 PMID:19249095
GEO:GPL2986
GEO:GSE10588
GEO:GSE10588|1 placenta severe preeclampsia normal pregnancy [placenta severe preeclampsia preeclampsia] Sitras et al. investigated the global placental gene expression profile in severe preeclampsia. Twenty-one women were randomly selected from 50 participants with uncomplicated pregnancies to match 21 patients with severe preeclampsia. Five preeclamptic placentas were excluded because of poor RNA quality, leaving 16 preeclamptic placentas for microarray experiments. Chorionic tissue was dissected from a standardised location—approximately 2 cm beside the umbilical cord insertion, from the middle layer of placenta midway between maternal and fetal surfaces—in order to reduce the bias related to the physiological difference in gene expression within the same placenta depending on the sampling site. 17 26 PMID:19249095
GEO:GPL2986
GEO:GSE10588
GEO:GSE9159|3 myometrium term labor preterm in labor with inflammation [myometrium cesarean section failure to progress term labor inflammation spontaneous preterm labor preterm premature rupture of membranes preterm labor] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE39043-4 endometrium early estrus (day 16) estrus (day 0) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE26315-3 amnion interleukin-1β challenge for 8 hours interleukin-1β challenge for 1 hour [amnion inflammation immune challenge cell culture] Using monolayer cultures of human amnion mesenchymal cells as a model, Li et al. aimed to detail the global programme of gene expression that occurs in response to cytokine challenge. Primary cultures of human amnion mesenchymal cells were prepared from amnion membranes obtained prior to labor at term and challenged with 10 ng/ml interleukin-1β for 1 hour or 8 hours in serum-free media, while control cells were treated with serum-free medium only. 3 3 PMID:21655103
GEO:GPL571
GEO:GSE26315
GEO:GSE56899-10 blood plasma postpartum third trimester pregnancy [maternal plasma normal pregnancy postpartum third trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE40182|4 cytotrophoblast preeclampsia cytotrophoblasts at 48 hours preterm labor cytotrophoblasts at 48 hours [cytotrophoblasts HELLP syndrome intrauterine growth restriction severe preeclampsia preeclampsia cell culture] Zhou et al. used global transcriptional profiling to explore mRNA changes that underlie cytotrophoblast (CTB) defects in preeclampsia. Villous CTBs were isolated from the placentas of women diagnosed with various forms of severe preeclampsia with or without intrauterine growth restriction, including superimposed hypertension and HELLP syndrome, and from the placentas of preterm labor patients with no signs of infection, which served as gestation-matched controls. Gene expression profiling was performed immediately after isolation and after 12, 24, and 48 hours in culture. 4 4 PMID:23934129
GEO:GPL570
GEO:GSE40182
GEO:GSE5999|B10 decidua 37-40 weeks pregnant 23-24 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE48424-3 blood severe preeclampsia non-severe preeclampsia [maternal blood severe preeclampsia preeclampsia] Textoris et al. used microarray profiling to study the transcriptional signature of blood samples associated with preeclampsia. The study included 13 women with severe preeclampsia, 6 women with non-severe preeclampsia, and 19 women with normal pregnancies. The criteria used to define severe preeclampsia included one of the following conditions: blood pressure higher than 160/110 mmHg, proteinuria higher than 1500 mg/24 h, maternal cerebral symptoms (seizures, stroke), intrauterine growth restriction below the 3° percentile, or multisystem disorder. Blood samples were collected from participants at the time of study inclusion. 12 5 PMID:24349325
GEO:GPL6480
GEO:GSE48424
ProteinAtlas - tissue: liver liver [tissue liver] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE5999[B]-6 decidua basal plate at 23–24 weeks basal plate at 18–19 weeks [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal–fetal interface during five gestational age intervals: 14–16, 18–19, 21, 23–24, and 37–40 weeks. Basal plate biopsy specimens were obtained from placentas after second trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE53669-1 umbilical cord blood umbilical cord blood antepartum maternal blood [umbilical cord blood maternal blood normal pregnancy antepartum gestational age] To detect unique fetal biomarkers in maternal blood, Maron et al. studied whole blood and plasma gene transcripts that were common to term pregnant women and their newborns but absent or reduced in the mothers postpartum. Maternal blood samples were obtained immediately prior to cesarean delivery and 24 to 36 hours postpartum. Umbilical cord blood samples were obtained at delivery. 13 12 PMID:17885688
GEO:GPL96
GEO:GSE53669
GEO:GSE46510|3 blood preterm birth at >7 days and <37 weeks spontaneous preterm birth within 48 hours [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. utilized microarray profiling to characterize whole blood gene expression in women with threatened preterm labor (TPTL). Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 15 48 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE30915-4 trophoblast BMP4-treated human embryonic stem cells at day 8 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE5999|A9 decidua 37-40 weeks pregnant 21 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL96
GEO:GSE5999
ProteinAtlas - tissue: smooth muscle smooth muscle tissue [tissue smooth muscle] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE39840-2 umbilical cord blood endotoxin-treated monocytes vehicle-treated control [umbilical cord blood monocytes immune challenge cell culture] Davidson et al. compared the gene expression profiles of endotoxin-stimulated neonatal polymorphonuclear leukocytes (PMNs) and monocytes (MONOs) to elucidate inflammatory control mechanisms in the newborns. Umbilical cord blood was obtained from placentas immediately after term elective cesarean deliveries. PMNs and MONOs were separately isolated from the same blood sample and treated with 10 ng/ml LPS (endotoxin) or with PBS (vehicle) for 4 hours. 5 5 PMID:23326478
GEO:GPL570
GEO:GSE39840
GEO:GSE24129-1 chorionic villus preeclamptic pregnancy normal pregnancy [placenta cesarean section preeclampsia] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
GEO:GSE4165-1 placenta dexamethasone-treated female vehicle-treated control [placenta fetal lung maturity antenatal corticosteroids dexamethasone drug treatment] To investigate the effects of antenatal corticosteroids like dexamethasone on placental function, Baisden performed a gene expression analysis on placentas from dexamethasone-treated pregnant mice and saline-treated controls. Pregnant females were injected with 0.5 mg/kg dexamethasone or an equivalent amount of saline on gestational days 15, 16, and 17. Gene expression profiles of placentas were assessed on day 20. 3 3 PMID:17559929
GEO:GPL339
GEO:GSE4165
GEO:GSE18809-1 placenta spontaneous preterm birth normal pregnancy [placenta spontaneous preterm birth] To test the hypthesis that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta, Chim et al. interrogated the mRNA levels of >50,000 genes and transcript variants in placentas collected from preterm spontaneous delivery (<34 weeks) and term spontaneous delivery (38–39 weeks) by gene expression microarray. Indicated preterm births, threatened preterm labor (term birth), multiple pregnancies, pregnancies complicated by preeclampsia, intrauterine growth restriction, fetal chromosomal and structural abnormalities were excluded from the study. A piece of placental tissue (about 0.1 cm³) was biopsied immediately after delivery. Care was taken to minimize the contamination of any maternal decidual tissue, fetal membranes, and blood clots in the biopsied placental tissue. 5 5 PMID:22496790
GEO:GPL570
GEO:GSE18809
GEO:GSE9984|3 chorionic villus third trimester pregnancy second trimester pregnancy [placenta normal pregnancy third trimester elective termination second trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45-59 days) and second trimester (109-115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the termination or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
GEO:GSE24129-3 chorionic villus fetal growth restriction preeclamptic pregnancy [placenta cesarean section fetal growth restriction preeclampsia] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
GEO:GSE9159|2 myometrium term not in labor preterm not in labor and no inflammation [myometrium cesarean section breech presentation preeclampsia] Weiner et al. sought the specific gene sets responsible for initiating term and preterm labor, along with the effector genes that are necessary for labor independent of gestation and underlying trigger. Myometrium was obtained from the upper pole of the transverse lower uterine segment incision of 4 groups of women at the time of their primary cesarean section: preterm not in labor and no inflammation (PTNL), preterm in labor with inflammation (PTL), term not in labor (TNL), and term labor (TL). Indications for cesarean delivery in the PTNL group were all related to preeclampsia and in the TNL were all related to breech presentation. The indication for cesarean delivery in the TL group was an arrest of cervical dilation at ≥6 cm. Patients in the PTL group all had intraamniotic inflammation. 3 3 PMID:20452493
GEO:GPL570
GEO:GSE9159
GEO:GSE25335-1 corpus luteum day 10 simulated early pregnancy day 10 untreated control [corpus luteum simulated early pregnancy chorionic gonadotrophin drug treatment] To explore chorionic gonadotrophin (CG)-regulated gene expression in the primate corpus luteum (CL) during simulated early pregnancy (SEP), Bishop et al. treated female rhesus monkeys with increasing dosages of hCG mimicking the rise detected during early pregnancy. SEP treatment began on day 9 of the luteal phase. The first day of the luteal phase was defined as the first day of low serum E (<100 pg/ml) following the mid-cycle E surge, with a coincident rise in serum P above 0.2 ng/ml. Individual CL were collected on days 10, 12, 15, and 18 of the luteal phase, representing 1, 3, 6 and 9 days of hCG treatment. Additionally, CL were collected from untreated monkeys on day 10 of the luteal phase to serve as baseline controls. 4 4 PMID:22072816
GEO:GPL3535
GEO:GSE25335
ProteinAtlas - tissue: rectum rectum [tissue rectum] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE26315-1 amnion interleukin-1β challenge for 1 hour untreated control [amnion inflammation immune challenge cell culture] Using monolayer cultures of human amnion mesenchymal cells as a model, Li et al. aimed to detail the global programme of gene expression that occurs in response to cytokine challenge. Primary cultures of human amnion mesenchymal cells were prepared from amnion membranes obtained prior to labor at term and challenged with 10 ng/ml interleukin-1β for 1 hour or 8 hours in serum-free media, while control cells were treated with serum-free medium only. 3 3 PMID:21655103
GEO:GPL571
GEO:GSE26315
ProteinAtlas - cell line: HaCaT HaCaT cell [cell line HaCaT] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE39043-6 endometrium late diestrus (day 12) early diestrus (day 3) [endometrium estrous cycle] Gebhardt et al. performed a microarray analysis of endometrial tissue samples from 5 normal-cycling warmblood mares to study the dynamics of equine endometrial gene expression. Samples were obtained by transcervical biopsy and taken at 5 different time points (days 0, 3, 8, 12, and 16) during the estrous cycle. 5 5 PMID:23077167
GEO:GPL15189
GEO:GSE39043
GEO:GSE24129|3 chorionic villus fetal growth restriction preeclamptic pregnancy [placenta cesarean section fetal growth restriction preeclampsia] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
GEO:GSE56899-1 blood plasma first trimester pregnancy non-pregnant control [maternal plasma normal pregnancy first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE9984-3 chorionic villus third trimester pregnancy second trimester pregnancy [placenta normal pregnancy cesarean section third trimester elective termination second trimester gestational age] Mikheev et al. used a whole genome approach to identify major functional categories of genes whose expression depends on gestational age. Gene expression profiles were compared in the villous tissues of first (45–59 days) and second trimester (109–115 days) placentas from uncomplicated elective termination versus cesarean section term placentas. Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, or abused alcohol or drugs. Any differences in drug exposure for the terminations or cesarean sections were not taken into consideration. 4 4 PMID:19050320
GEO:GPL570
GEO:GSE9984
GEO:GSE7586-2 chorionic villus chronic placental malaria (inflammation) uninfected control (no inflammation) [placenta inflammation infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 7 9 PMID:17579077
GEO:GPL570
GEO:GSE7586
ProteinAtlas - cell line: RT4 RT-4 cell [cell line RT4] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE7586-3 chorionic villus chronic placental malaria (inflammation) acute placental malaria (no inflammation) [placenta inflammation infection placental malaria pregnancy-associated malaria] Muehlenbachs et al. performed a genome-wide analysis of the local human response to sequestered malaria parasites in order to identify genes associated with chronic placental malaria (PM). Placental samples from 20 first time mothers were selected based on PM status and RNA quality. A full thickness biopsy was made from the middle third of the placental disc, and placental villi were dissected at <0.5 mm³, excluding large vessels, stem villi, infarcts, fetal membranes, or decidua from placental tissues. 7 3 PMID:17579077
GEO:GPL570
GEO:GSE7586
GEO:GSE56899-4 blood plasma postpartum non-pregnant control [maternal plasma normal pregnancy postpartum gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 4 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE30915-5 trophoblast BMP4-treated human embryonic stem cells at day 10 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE44711-1 chorionic villus early-onset preeclampsia gestational age-matched control [chorionic villus early-onset preeclampsia preeclampsia] Blair et al. investigated the DNA methylation and gene expression of chorionic villi samples from early-onset preeclampsia (EOPET) placentas compared to gestational age-matched controls. Control placentas were obtained from chromosomally normal losses or births due to a mix of etiologies (premature rupture of membranes, loss of amniotic fluid and cervical incompetence) with no evidence of placental abnormality based on a pathological exam. Gene expression data were obtained using a subset of EOPET samples and controls that were also run on the 450K array. Chorionic villi were sampled from at least two sites (center and perimeter) on the fetal side of the placenta. 8 8 PMID:23770704
GEO:GPL10558
GEO:GSE44711
GEO:GSE30915-6 trophoblast BMP4-treated human embryonic stem cells at day 12 BMP4-treated human embryonic stem cells at day 0 [trophoblasts embryonic stem cells differentiation cell culture] Marchand et al. performed a large-scale microarray analysis to understand changes in the transcriptome during the differentiation of human embryonic stem cells (hESCs) down the trophoblast lineage. HESCs, obtained from WiCell Research Institute, were cultured with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyzed for differentiation every 2 days. 3 3 PMID:21368299
GEO:GPL6244
GEO:GSE30915
GEO:GSE5999|B8 decidua 23-24 weeks pregnant 21 weeks pregnant [basal plate normal pregnancy elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 6 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE7971-1 corpus luteum PGF2α-treated female vehicle-treated control [corpus luteum luteolysis drug treatment] To delineate the mechanism of PGF2α-induced luteolysis, Priyanka et al. studied the changes in global gene expression within the corpus luteum following PGF2α treatment in female bonnet monkeys. Female monkeys were treated with PGF2α or PBS (vehicle) via three injections on day 10 of the luteal phase, and corpus luteum samples were collected following 24 hours. 3 3 PMID:18988674
GEO:GPL3535
GEO:GSE7971
GEO:GSE56899-6 blood plasma third trimester pregnancy first trimester pregnancy [maternal plasma normal pregnancy third trimester first trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE57733-1 decidua endometriosis-affected pregnancy normal pregnancy [choriodecidua cesarean section endometriosis] Marcellin et al. explored changes in the choriodecidua of women with endometriosis through genomic and epigenomic microarray analyses in order to gain insight into the intrinsic molecular mechanisms involved in endometriosis. Cases, all affected with painful deep infiltrating endometriosis, were either operated before pregnancy for complete surgical resection of the endometriotic lesions, or had a complete imaging workup before pregnancy that confirmed the diagnosis of endometriosis. Controls samples were collected from women without past history of either endometriosis or chronic pelvic pain. All women were delivered by cesarean section at term before labor for obstetrical indication following an uneventful pregnancy. Collected fetal membranes were separated from the placenta, and choriodecidua was peeled from the amnion and appropriately prepared for RNA and DNA extractions. 3 3 PMID:25432921
GEO:GPL17425
GEO:GSE57733
GEO:GSE5999|B7 decidua 37-40 weeks pregnant 18-19 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 9 PMID:17170095
GEO:GPL97
GEO:GSE5999
ProteinAtlas - cell line: U-937 U-937 cell [cell line U-937] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE31329|1 myometrium myometrium under high tension myometrium under low tension [myometrium tissue culture] Tattersall et al. aimed to identify factors that mediate the effect of stretch on human myometrium. The study obtained myometrial samples from non-laboring patients, undergoing routine elective cesarean section at 38-40 weeks of pregnancy, for microarray analysis. Human myometrial explants were maintained in prolonged culture (65 hours) under either low tension (0.6 g) or high tension (2.4 g). Following culture, the samples were trimmed to remove tissue that had not been incubated under tension, snap frozen in liquid nitrogen, and stored at −80 °C. 9 9 PMID:22411014
GEO:GPL6883
GEO:GSE31329
GEO:GSE56899-9 blood plasma postpartum second trimester pregnancy [maternal plasma normal pregnancy postpartum second trimester gestational age] Koh et al. performed a longitudinal study on pregnant women that analyzed their combined cell-free RNA transcriptomes across all three trimesters of pregnancy and after delivery. Plasma samples were collected from 4 non-pregnant subjects (2 men and 2 women), as well as from 11 pregnant women who contributed samples at the first, second, and third trimesters and postpartum. 11 11 PMID:24799715
GEO:GPL6244
GEO:GSE56899
GEO:GSE24129-2 chorionic villus fetal growth restriction normal pregnancy [placenta cesarean section fetal growth restriction] To investigate the mechanisms underlying preeclampsia and unexplained fetal growth restriction (FGR), Nishizawa et al. performed global gene expression profiling on placental tissue from severe preeclamptic pregnancies and normotensive pregnancies with or without FGR. FGR was diagnosed when the birth weight was below the 10th percentile of that anticipated for the given gestational age for a Japanese population. To avoid any effects of labor upon the gene expression profiles of the tissue samples, all of the placental biopsies were obtained following cesarean sections from women who had not undergone labor. In normotensive cases, cesarean sections were performed due to previous cesarean sections. After removal of the maternal deciduas and amniotic membranes, 1 cm sections of placental villi were dissected from the four different central areas between the basal and chorionic plates. 8 8 PMID:21810232
GEO:GPL6244
GEO:GSE24129
GEO:GSE5999|B9 decidua 37-40 weeks pregnant 21 weeks pregnant [basal plate cesarean section normal pregnancy third trimester elective termination second trimester gestational age] Winn et al. profiled gene expression at the human maternal-fetal interface during five gestational age intervals: 14-16, 18-19, 21, 23-24, and 37-40 weeks. Basal plate biopsy specimens were obtained from placentas after second-trimester elective terminations of singleton pregnancies or normal nonlabored singleton pregnancies. Pregnancies complicated by fetal anomalies, hypertension, diabetes, or other significant maternal health issues were excluded. 9 6 PMID:17170095
GEO:GPL97
GEO:GSE5999
GEO:GSE61822|1 chorion neurocognitive impairment no neurocognitive impairment [chorioamniotic membrane preterm birth neurocognitive impairment] To determine if neonates who developed neurocognitive impairment can be identified at birth, Pappas et al. conducted a retrospective case-control study that characterized the chorioamniotic membranes of 66 very preterm neonates with or without neurocognitive impairment by microarray profiling. Chorioamniotic membrane samples were retrieved from the biological sample bank of Wayne State University and the Perinatology Research Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development. Cases and controls were singleton neonates born between 23-32 weeks of gestation matched for gestational age. Neurocognitive impairment was defined by a cognitive composite score of <80 with or without associated neuromotor impairment at 18–24 months’ corrected age according to the Bayley Scales of Infant Development, 3rd Edition. 13 14 PMID:25822971
GEO:GPL10558
GEO:GSE61822
ProteinAtlas - cell line: U-87 MG U-87MG cell [cell line U-87 MG] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: TIME cell culture [cell line TIME] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - tissue: gallbladder gall bladder [tissue gallbladder] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
ProteinAtlas - cell line: U-251 MG U-251 MG cell [cell line U-251 MG] 44 cell lines and 32 tissues. For cell lines, early-split samples were used as duplicates and total RNA was extracted using the RNeasy mini kit. All tissues were from the Uppsala Biobank and RNA samples were extracted from frozen tissue sections. For a total of 91 cell line samples and 122 tissue samples, mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines using the standard Illumina RNA-Seq protocol with a read length of 2x100 bases. Transcript abundance was estimated using Tophat v2.0.8b and Cufflinks v2.1.1. For each gene, the average FPKM value for replicate samples were used as abundance scores. The threshold to detect gene was > 1 FPKM. PMID: 25613900
GEO:GSE4165|1 placenta dexamethasone treatment vehicle treatment [placenta fetal lung maturity antenatal corticosteroids dexamethasone drug treatment] To investigate the effects of antenatal corticosteroids like dexamethasone (DEX) on placental function, Baisden et al. treated pregnant C57/BL6 mice with DEX (0.5 mg/kg) on gestational days 15, 16, and 17 and studied changes in placental gene expression by microarray profiling. Gene expression profiles of DEX-treated placentas and saline-treated controls were assessed on gestational day 20. 3 3 PMID:17559929
GEO:GPL339
GEO:GSE4165
GEO:GSE9773-1 cytotrophoblast first trimester extravillous trophoblasts first trimester villous cytotrophoblasts [cytotrophoblasts first trimester trophoblast invasion cell culture] To gain more insight into the regulatory mechanisms of trophoblast invasion, Bilban et al. investigated the genome-wide expression profiles of nonmigratory villous cytotrophoblasts and invasive, extravillous trophoblasts. Villous cytotrophoblasts were purified from first trimester placentas and grown in culture for 24 hours. Extravillous trophoblasts were collected from first trimester villous explant cultures seeded on Matrigel after 72 hours. 6 5 PMID:18845641
GEO:GPL96
GEO:GSE9773
GEO:GSE54618-3 placenta preeclamptic + HELLP pregnancy preeclamptic pregnancy [placenta HELLP syndrome preeclampsia] To identify genes and pathways correlating with β-glucocerebrosidase (GBA) expression, Jebbink et al. performed microarray expression profiling on placental tissue from normotensive patients with low GBA expression and from preeclamptic patients with high GBA expression. Quantitative RT-PCR was used to determine normotensive and preeclamptic placentas with the most extreme levels of GBA expression prior to microarray analysis. Placental biopsies were obtained immediately after delivery from a macroscopically viable (non-infarcted) central cotyledon from the maternal side. 7 4 PMID:25552189
GEO:GPL10558
GEO:GSE54618
GEO:GSE46510-6 blood term delivery preterm birth after 48 hours and within 7 days [maternal blood term delivery preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 79 12 PMID:24828675
GEO:GPL16311
GEO:GSE46510
GEO:GSE46510-1 blood spontaneous preterm birth within 48 hours no spontaneous preterm birth within 48 hours [maternal blood preterm birth spontaneous preterm birth threatened preterm labor] Heng et al. characterized the gene expression profiles of whole blood from women with threatened preterm labor. Peripheral blood was collected at point of hospital admission from 154 women with threatened preterm labor before any medical treatment. Participants were stratified into two groups: spontaneous preterm birth (sPTB) within 48 hours of hospital admission and no sPTB within 48 hours. Exclusion criteria included excessive antepartum hemorrhage, preterm prelabor rupture of membranes, clinical chorioamnionitis, fetal anomaly, preeclampsia, intrauterine growth restriction, diabetes mellitus, gestational diabetes, or multi-fetal pregnancy. 48 106 PMID:24828675
GEO:GPL16311
GEO:GSE46510