Transcriptomics

Dataset Information

303

RNA-seq transcriptomes of term not in labour and term in labour human myometrial tissue


ABSTRACT: Purpose: To chart the human myometrial transcriptomes before and after the onset of labour. Methods: Tophat splice junction mapping of paired-end reads, HTSeq to generate counts, cufflinks to track transcripts, DESeq, edgeR and baySeq to detect differentially expressed genes and principal component analysis for clustering analyses. Results: We mapped on average 14 million paired-end reads per sample (counting each end individually) to the human genome (build hg19) and covered the expressed transcriptome about 13 times with a TopHat-HTSeq workflow. We performed a comparative analysis with an analogous microarray study (Mittal et al., 2010) and found some overlap between the RNA-seq and the microarray data. Conclusions: Our study is the first RNA-seq study of the human myometrium before and after the onset of labour. We show that while microarray and RNA-seq studies may complement each other, RNA-seq has a much greater resolution. At term with and at term without labour human myometrial mRNA profiles were generated by deep sequencing, using Illumina GAIIx (five biological replicates each).

ORGANISM(S): Homo sapiens  

SUBMITTER: Jonathan D Moore   Andrew Blanks  Siobhan Quenby  Yi-Wah Chan  Hugo van den Berg 

PROVIDER: E-GEOD-50599 | ArrayExpress | 2014-02-17

SECONDARY ACCESSION(S): GSE50599SRP029592PRJNA218059

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq.

Chan Yi-Wah YW   van den Berg Hugo A HA   Moore Jonathan D JD   Quenby Siobhan S   Blanks Andrew M AM  

Experimental physiology 20131122 3


The transition of the human uterus from a quiescent to a contractile state takes place over a number of weeks. On such biological time scales, cellular phenotype is modified by changes in the transcriptome, which in turn is under the control of the underlying endocrine, paracrine, and biophysical processes resulting from the ongoing pregnancy. In this study, we characterize the transition of the human myometrial transcriptome at term from not in labour (NIL) to in labour (LAB) using high through  ...[more]

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