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Series GSE42398 Query DataSets for GSE42398
Status Public on Dec 17, 2012
Title Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (~8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3'READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3' end–processing activity in development and differentiation.
Overall design 3'READS to map pAs in mouse genome
Contributor(s) Hoque M, JI Z, Zheng D, Luo W, Li W, You B, Park JY, Yehia G, Tian B
Citation(s) 23241633
Submission date Nov 19, 2012
Last update date May 15, 2019
Contact name Zhe Ji
Organization name Northwestern University
Street address 303 E Superior St, Lurie 6-107
City Chicago
State/province ILLINOIS
ZIP/Postal code 60611
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1039195 CU5T45 Cell line mix 1 (3'READS)
GSM1039196 RegularOligo(dT) Cell line mix 1 (3'READS)
GSM1039197 CLIP-seq Cstf64 replicate 1 (CLIP-seq)
BioProject PRJNA181289
SRA SRP017249

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Supplementary file Size Download File type/resource
GSE42398_RAW.tar 17.1 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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