Term W/O labor fetal membrane mRNA expression patterns
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Corinne Belville
PROVIDER: E-MTAB-10516 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The purpose of our study was to characterize methylomic status by comparing the zone of fetal membranes (site of rupture (ZAM) and away from the site (ZIM)) and the tissue layer (amnion and choriodecidua). Nine fetal membranes were collected by cesarean section at term before labor. . After classifying genes in specific biological processes, we highlight particular patterns like inflammation.
2022-02-03 | E-MTAB-10520 | biostudies-arrayexpress
Project description:To characterize the molecular signature of the choriodecidua remodeling in late pregnancy befour labour, we have employed whole genome microarray expression profiling to identify genes that sign for fetal membranes remodeling. Fetal membranes were collected from healthy women, after an uncomplicated pregnancy, undergoing a planned cesarean delivery at term, for feto-pelvic disproportion or scarred uterus. During surgery, a Kocher's forceps was placed on membranes overlying the cervix and the swelling area surrounding the forceps was dissected in the operating room under sterile conditions, the site, pinched by the forceps, being discarded. Fetal membranes in a remote zone were also sampled. Isolated RNAs were hybridized to the Aligent SurePrint G3 Human GE 8x60K Microarray. Two independent bio-analyses singularize a signature in the zone of altered morphology for Graft vs Host Disease and leukocyte activation, arguing for a focal loss of maternal-fetal tolerance. This was further confirmed by flow cytometry, electron microscopy, and immuhistochemistry analyses.
2016-11-25 | GSE50900 | GEO
Project description:To characterize the molecular signature of the choriodecidua remodeling in third trimestry of pregnancy before labour, we have employed whole genome microarray expression profiling. Fetal membranes were collected from women undergoing a emergency cesarean delivery before term (before 32 weeks of gestation and between 33-35 weeks of gestation), for preeclampsia and/or in utero growth retardation. During surgery, a Kocher's forceps was placed on membranes overlying the cervix and the area surrounding the forceps was dissected in the operating room under sterile conditions, the site, pinched by the forceps, being discarded. Fetal membranes in a remote zone were also sampled. Isolated RNAs were hybridized to the Aligent SurePrint G3 Human GE 8x60K Microarray.
2016-11-25 | GSE59686 | GEO
Project description:We compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with preterm prelabor rupture of membranes (PPROM) deliveries to further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events. Chorioamnion, separated into amnion and chorion, was collected from gestationally age-matched cases and controls within 15 minutes of birth, and analyzed using RNA sequencing. In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.
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Project description:Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes
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Project description:Amniotic fluid volume (AFV) is determined primarily by the rate of intramembranous (IM) transport of AF cross the amnion. Intramembranous transport is characterized as vesicular endocytotic and transcytotic processes regulated by fetal urine-derived stimulators and AF inhibitors. Our objectives were to utilize a large-scale multiomics approach to decipher the vesicular transport pathways in the amnion and to identify potential transport regulators in AF and fetal urine. We utilized fetal sheep to experimentally induce alterations in IM transport rate and analyze the expression profiles of transcripts and proteins in amnion, AF and fetal urine. Four experimental groups were studied: control (C), urine drainage with reduced IM transport rate and AFV (UD), urine drainage and fluid replacement with decreased IM transport rate but increased AFV (UDR), and intra-amniotic fluid infusion with increased IM transport rate and AFV (IA). Amnion and fluid samples were subjected to transcriptomics (RNA-Seq) and isobaric labeling proteomics studies followed by bioinformatics analyses using Ingenuity Pathway Analysis software. The analyses revealed 9 functional transport pathways and a panel of differentially expressed transcripts and proteins that are known mediators of vesicular transport and cellular trafficking. During UD, expression of transport and trafficking mediators were reduced as compared to controls. With UDR, expression of energy metabolism activators increased while trafficking mediators decreased. During IA, expression of vesicular uptake molecules increased while trafficking mediators decreased. Co-expression of the motor protein, cytoplasmic dynein light chain-1, in both AF and fetal urine suggest that this molecule may function as a urine-derived stimulator of IM transport.
2021-07-21 | PXD013135 | Pride
Project description:We have characterized two post-translational histone modifications in C. elegans on a genomic scale. Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing to obtain positional and coverage maps. Two methylated histone H3 populations were chosen for comparison: H3K4 histone methylation (associated with active chromosomal regions) and H3K9 histone methylation (associated with inactivity). From analysis of the sequence data, we found nucleosome cores with these modifications to be enriched in two distinct partitions of the genome; H3K4 methylation was particularly prevalent in promoter regions of widely-expressed genes while H3K9 methylation was enriched on specific chromosomal arms. For each of the six chromosomes, the highest level of H3K9 methylation corresponds to the pairing center responsible for chromosome alignment during meiosis. H3K9 enrichment at pairing centers appears to be an early mark in meiotic chromosome sorting, occurring in the absence of components required for proper pairing of homologous chromosomes. H3K9 methylation shows an intricate pattern within the chromosome arms, with a particular anti-correlation to regions that display a strong ~10 bp periodicity of AA/TT dinucleotides that is known to associate with germline trancription. By contrast to the global features observed with H3K9 methylation, H3K4 methylation profiles were most striking in their local characteristics around promoters, providing a unique promoter-central landmark for 3903 C. elegans genes and allowing a precise analysis of nucleosome positioning in the context of transcriptional initiation. Keywords: epigenetics Examination of total nucleosome and nucleosomes with 2 different histone modifications in C. elegans. 5 samples are analyzed: 1. total mononucleosome core DNA from C. elegans wild type strain N2, 2. anti-H3K4me2/3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 3. anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 4. total mononucleosome core DNA from C. elegans mutant strain zim-2(tm-574), 5. anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans mutant strain zim-2(tm-574)
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Project description:Approximately 25% of all preterm births are due to preterm premature rupture of membranes. Mice deficient in proteoglycans biglycan (Bgn) and decorin (Dcn) display abnormal fetal membranes and increased incidence of preterm birth. We conducted RNA-Seq to profile fetal membranes and identify molecular pathways that may lead to preterm birth in double knockout (DKO) mice (Bgn −/−; Dcn −/− ) compared to wild-type (WT) at two different gestational stages, E12 and E18 (n=3 in each group). 3264 transcripts were differentially regulated in E18 DKO vs. WT fetal membranes, and 96 transcripts differentially regulated in E12 DKO vs. WT fetal membranes (FDR<0.05, log 2 FC≥1). Differentially regulated transcripts in E18 DKO fetal membranes were significantly enriched for genes involved in cell cycle regulation, extracellular matrix-receptor interaction, and the complement cascade. 50 transcripts involved in the cell cycle were altered in E18 DKO fetal membranes (40↓, 10↑, FDR<0.05), including p21 and p57 (↑), and Tgfb2, Smad3, CycA, Cdk1, and Cdk2(↓). Thirty-one transcripts involved in the complement cascade were altered (11↓, 20↑, FDR<0.05) in E18 DKO fetal membranes, including C1q, C2, and C3 (↑). Differentially expressed genes in the top three molecular pathways (1) showed evidence of negative or purifying selection, and (2) were significantly enriched (Z-score>10) for transcription factor binding sites for Nr2f1 at E18. We propose that in DKO mice, cell cycle arrest results in lack of cell proliferation in fetal membranes, inability to contain the growing fetus, and preterm birth.
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Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of zim was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
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