|
| 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.
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| |
|
| 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 |
| E-mail(s) |
[email protected], [email protected]
|
| 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) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
| GPL14954 |
Illumina HiSeq 2000 (Macaca mulatta) |
| GPL15749 |
Illumina HiSeq 2000 (Bos taurus) |
| GPL16133 |
Illumina HiSeq 2000 (Gallus gallus) |
|
| Samples (134)
|
|
| Relations |
| BioProject |
PRJNA177791 |
| SRA |
SRP016501 |
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