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SRP029592
Homo sapiens
10 Downloadable Samples
Illumina Genome Analyzer IIx
Description
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. 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).
Publication Title
Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 29 Downloadable Samples
- Illumina HiSeq 2500
Description
We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control. Overall design: We crossed UAS-unc84-2XGFP transgenic flies with 10 different GAL4 drivers (Dh44-GAL4, NPF-GAL4, NPFR-GAL4, Tdc2-GAL4, Crz-GALl4, TH-GAL4, Trh-GAL4, Fru-GAL4, OK107-GAL4, and elav-GAL4), immunoprecipitated tagged nuclei and extracted RNA. Three independent replicates of each each cross were performed to isolate RNA for RNA-sequencing.
Publication Title
Illuminating spatial A-to-I RNA editing signatures within the <i>Drosophila</i> brain.
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Subject
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