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| Status |
Public on Feb 17, 2014 |
| Title |
RNA-seq transcriptomes of term not in labour and term in labour human myometrial tissue |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
At term with and at term without labour human myometrial mRNA profiles were generated by deep sequencing, using Illumina GAIIx (five biological replicates each).
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| Contributor(s) |
Chan Y, van den Berg H, Moore JD, Quenby S, Blanks A |
| Citation(s) |
24273302, 27105427 |
| |
| Submission date |
Sep 05, 2013 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Andrew Blanks |
| E-mail(s) |
Andrew.Blanks@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Department |
Warwick Medical School
|
| Lab |
Division of Reproductive Health
|
| Street address |
Clifford Bridge Road
|
| City |
Coventry |
| ZIP/Postal code |
CV2 2DX |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA218059 |
| SRA |
SRP029592 |
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