Term and preterm shotgun samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1549320_1.fastq.gz | Fastqsanger.gz | |||
| ERR1549320_2.fastq.gz | Fastqsanger.gz | |||
| ERR1549321_1.fastq.gz | Fastqsanger.gz | |||
| ERR1549321_2.fastq.gz | Fastqsanger.gz | |||
| ERR1549323_1.fastq.gz | Fastqsanger.gz |
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Project description:Distinct processes govern the transition from myometrial quiescence to activation during both term and preterm labor. We sought the specific gene sets responsible for initiating term and preterm labor, along with a core set of effector genes necessary for labor independent of gestational age and the underlying trigger. The Effector Gene Set consisted of 49 genes present in both preterm and term labor but absent from non-labor samples. 122 genes were specific to preterm labor (Preterm Initiator Set) and 229 to term labor (Term Initiator Set). The Term Initiator and the Effector Sets reflected predominantly inflammatory processes. Surprisingly, the Preterm Initiator Gene Set reflected molecular and biological events almost exclusive of inflammation. Preterm and term labor differ dramatically in their unique, initiator gene profiles, suggesting alternative pathways underlie these events. Inflammatory processes are ubiquitous to the Term Initiator and the Effector Gene Sets, supporting the idea term parturition is an inflammatory process. The absence of inflammatory processes in the Preterm Initiator Set suggests inflammation is secondary to processes triggering spontaneous preterm birth, and could explain the lack of therapeutic efficacy associated with anti inflammatory/antibiotic regimens. Experiment Overall Design: Myometrial gene expression was analyzed from samples obtained at term (n=6) or preterm (n=6) with and without labor using cDNA microarrays. Patients in preterm labor all had intra amniotic inflammation. Gene sets were generated using logical operations within a functional mapping tool (MetaCoreâ¢, GeneGo, St. Joseph, MI). Relevant gene sets were validated with quantitative real-time polymerase chain reaction.
2008-10-26 | E-GEOD-9159 | biostudies-arrayexpress
Project description:This study evaluates the gene expression patterns in 36 decidual samples of women having gone through different types of child birth. The samples were profiled on Illumina Human HT-12_v4 BeadArrays. The analysis includes quality control and exploratory analysis of the dataset, followed by the identification of differentially expressed genes (DEGs) and finally, functional analysis for enrichment of KEGG pathways and GO terms amongst the DEGs. The statistical analysis was performed for six comparisons: Term labour (TL) vs Term not labour (TNL), TL vs Preterm labour (PTL), TL vs Preterm non-labour (PTNL), TNL vs PTL, TNL vs PTNL and PTL vs PTNL. This study evaluates the gene expression levels from decidual samples obtained from women giving birth with different types of labour. The dataset was composed of 36 Illumina Human HT-12_v4 expression BeadArrays.
2017-08-23 | E-MTAB-5353 | biostudies-arrayexpress
Project description:Distinct processes govern the transition from myometrial quiescence to activation during both term and preterm labor. We sought the specific gene sets responsible for initiating term and preterm labor, along with a core set of effector genes necessary for labor independent of gestational age and the underlying trigger. The Effector Gene Set consisted of 49 genes present in both preterm and term labor but absent from non-labor samples. 122 genes were specific to preterm labor (Preterm Initiator Set) and 229 to term labor (Term Initiator Set). The Term Initiator and the Effector Sets reflected predominantly inflammatory processes. Surprisingly, the Preterm Initiator Gene Set reflected molecular and biological events almost exclusive of inflammation. Preterm and term labor differ dramatically in their unique, initiator gene profiles, suggesting alternative pathways underlie these events. Inflammatory processes are ubiquitous to the Term Initiator and the Effector Gene Sets, supporting the idea term parturition is an inflammatory process. The absence of inflammatory processes in the Preterm Initiator Set suggests inflammation is secondary to processes triggering spontaneous preterm birth, and could explain the lack of therapeutic efficacy associated with anti inflammatory/antibiotic regimens. Keywords: myometrial gene expression, preterm versus term labor
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Project description:Genome wide placental DNA methylation profiling of full term and preterm deliveries sampled from 5 full term deliveries and 4 preterm deliveries. The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in formalin fixed samples. Samples included 4 placental tissues from 4 women with preterm delivery and 5 placental tissues from 5 women with full term delivery. 9 women's placental DNA (4 women had perterm deliveries and 5 women had full term deliveries) were hybridised to the Illumina HumanMethylation450 Beadchip
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Project description:Preterm birth is multifactorial in origin with several distinct clinical phenotypes of differing etiologies, including idiopathic preterm birth. Preterm birth involves the interaction of genetic, societal and environmental factors such as nutrition, lifestyle and stress that may modulate the length of gestation via the epigenome. DNA methylation is a well-studied epigenetic modification whereby promoter methylation commonly represses gene expression and vice versa. Myometrial tissue was obtained at cesarean section at term with or without labor, preterm without labor, idiopathic preterm labor, and twin gestations with labor. Differences in the myometrial epigenomes were identified at gene promoters, CpG islands, CpG island shores and shelves, gene bodies across the genome between the groups of women with preterm labor of different phenotypes vs. normal term labor. Functional clustering analysis indicated the significantly enriched pathways of hypomethylated genes (permissive) were related to acute inflammatory and acute-phase responses. By contrast, genes that are hypermethylated (repressive) revealed enrichment for contractile fibers and cell. This study provides the first high-resolution DNA methylome of human myometrium with evidence for differences in the methylome that may relate to idiopathic preterm birth via regulation of gene expression. The findings extend previous observations that idiopathic preterm labor is associated with subclinical intrauterine infection and inflammatory pathways and point to targets for further molecular characterization of preterm delivery. Comparison of the human myometrial epigenomes in pregnancies with preterm labor of different phenotypes vs. normal term labor
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