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Series GSE41637 Query DataSets for GSE41637
Status Public on Dec 21, 2012
Title Evolutionary dynamics of gene and isoform regulation in mammalian tissues
Organisms Gallus gallus; Macaca mulatta; Bos taurus; Mus musculus; Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling.
Overall design Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)
Contributor(s) Merkin JJ, Burge CB
Citation(s) 23258891
Submission date Oct 17, 2012
Last update date May 15, 2019
Contact name Jason Merkin
Organization name MIT
Department Biology
Lab Burge
Street address 31 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (7)
GPL10669 Illumina Genome Analyzer IIx (Rattus norvegicus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (134)
GSM1020640 mouse_a_brain
GSM1020641 mouse_a_colon
GSM1020642 mouse_a_heart
BioProject PRJNA177791
SRA SRP016501

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41637_RAW.tar 5.3 Gb (http)(custom) TAR (of GTF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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