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| Status |
Public on Feb 26, 2011 |
| Title |
RNA polyadenylation landscape in human and mouse cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs.
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| Overall design |
We first analyzed HeLa cell transcriptome using PAS-Seq to demonstrate that PAS-Seq not only accurately and comprehensively identifies poly(A) junctions, but also provide quantitative information on the relativel abundance of APA isoforms. Next we analyzed the mouse embryonic stem cells, neural stem/progenitor cells, and neurons by PAS-Seq to characterize the dynamic changes of mRNA polyadenylation during stem cell differentiation.
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| |
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| Contributor(s) |
Shi Y |
| Citation(s) |
21343387 |
| Submission date |
Nov 17, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Shepard |
| E-mail(s) |
peter.shepard@gmail.com
|
| Organization name |
University of California, Irvine
|
| Department |
M&G
|
| Lab |
Shi Lab
|
| Street address |
Med Sci B233
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697-4025 |
| Country |
USA |
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| Platforms (2) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (4)
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| Relations |
| SRA |
SRP005177 |
| BioProject |
PRJNA133813 |
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