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Series GSE25450 Query DataSets for GSE25450
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.
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.
Contributor(s) Shi Y
Citation(s) 21343387
Submission date Nov 17, 2010
Last update date May 15, 2019
Contact name Peter Shepard
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
Platforms (2)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (4)
GSM624686 HeLa-PASSeq
GSM624687 ES-PASSeq
GSM624688 NSP-PASSeq
SRA SRP005177
BioProject PRJNA133813

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Supplementary file Size Download File type/resource
GSE25450_PAS-seq-1.pdf.gz 85.8 Kb (ftp)(http) PDF
GSE25450_hela_custom_track.txt.gz 644.5 Kb (ftp)(http) TXT
GSE25450_mouse_track.txt.gz 2.1 Mb (ftp)(http) TXT
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