Transcriptomics

Dataset Information

301

RNA polyadenylation landscape in human and mouse cells


ABSTRACT: 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. 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.

ORGANISM(S): Musculus  

SUBMITTER: Peter Shepard   Yongsheng Shi 

PROVIDER: E-GEOD-25450 | ArrayExpress | 2011-02-26

SECONDARY ACCESSION(S): GSE25450SRP005177PRJNA133813

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq.

Shepard Peter J PJ   Choi Eun-A EA   Lu Jente J   Flanagan Lisa A LA   Hertel Klemens J KJ   Shi Yongsheng Y  

RNA (New York, N.Y.) 20110222 4


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 polyade  ...[more]

Similar Datasets

2011-02-26 | GSE25450 | GEO
2016-08-14 | E-GEOD-84170 | ArrayExpress
2012-12-17 | E-GEOD-42398 | ArrayExpress
2015-04-01 | E-GEOD-62001 | ArrayExpress
| GSE84461 | GEO
| GSE90517 | GEO
| GSE67649 | GEO
2015-06-30 | E-GEOD-39051 | ArrayExpress
| GSE87914 | GEO
| GSE85368 | GEO