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GSE34204
Homo sapiens
32 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Transcript abundance results from the balance between transcription and mRNA decay, and varies pervasively in humans. We have examined the effect of DNA variation on mRNA half-life differences by conducting a genome-wide survey of mRNA stability in seven human HapMap lymphoblastoid cell lines (LCLs). We determined the mRNA half-life for each gene from the ratio of 4-thio-uridine (4sU)-labeled nascent RNAs to total RNAs. 5,145 (46%) of 11,132 analyzed genes showed inter-individual mRNA half-life differences at a false discovery rate, FDR<0.05. As previously reported, we found transcription to be the main factor influencing transcript abundance. Although mRNA half-life explained only ~6% of transcript abundance on average, it explained ~16% for the subset of genes (~10%) showing inter-individual mRNA half-life differences (P<0.001). We confirmed previously reported correlations of mRNA half-life with transcript length, 3-UTR length, and number of exon-junctions per kb of transcript. The number of miRNA targets in 3-UTRs was negatively correlated with half-life (P=2.210-16), a new observation that is consistent with the role of miRNA in inducing mRNA degradation. Notably, coding GC and GC3 content showed positive correlations with mRNA half-life in genes with inter-individual mRNA half-life differences, implying a role of mRNA stability in shaping synonymous codon usage bias. Consistently, G or C alleles of coding SNPs were found associated with longer mRNA half-life (P=0.021). As expected, we also found that nonsense SNPs were associated with shorter mRNA half-life (P=0.009). Our results strongly suggest that inter-individual mRNA stability differences are widespread and affected by DNA sequence and composition variation.
Publication Title
Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines.
Sample Metadata Fields
Disease, Cell line
View Samples- Homo sapiens
- 15 Downloadable Samples
Ion Torrent Proton
Description
Tumor-infiltrating macrophages, NK cells, CD8+ and CD4+ T cells sorted from clear cell renal cell carcinoma patient specimens. Overall design: 4 macrophage samples (CD45+CD3-CD56-CD14+), 2 CD16+ NK cell samples (CD45+CD3-CD56+CD16+), 5 CD8+ T cell samples (CD45+CD3+CD8+), 3 CD4+ T cell samples (CD45+CD3+CD4+), and one non-immune cell sample (CD45-).
Publication Title
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples