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Series GSE23694 Query DataSets for GSE23694
Status Public on Nov 07, 2010
Title Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of confidence in these estimates. Incorporation of the length distribution of inserted cDNA fragments in paired-end RNA-Seq analysis in MISO enables dramatic improvements in estimation of alternative splicing levels relative to previous methods. We show that one lane of paired-end RNA-Seq data can provide far more information about splicing than two lanes of single-end data, depending critically on properties of the distribution of cDNA fragment lengths in the sequenced library. MISO also leads to an intuitive method to detect differentially regulated exons or isoforms. Application of this method implicates the RNA splicing factor hnRNP H in regulation of alternative cleavage and polyadenylation, a role that is supported by UV crosslinking/immunoprecipitation/high-throughput sequencing (CLIP-Seq) analysis. Together, our results provide a probabilistic framework for RNA-Seq analysis, derive functional insights into pre-mRNA processing, and yield guidelines for the optimal design of RNA-Seq experiments for studies of gene and isoform expression.
Overall design CLIPseq of hnRNP H in HEK 293T cells.
RNAseq of polyA+ RNA from C2C12 mouse myoblasts stably expressing an empty vector or a vector containing an shRNA against CUGBP1. Libraries of two different insert lengths were created and examined.
Contributor(s) Katz Y, Wang ET, Airoldi E, Burge C
Citation(s) 21057496
Submission date Aug 18, 2010
Last update date May 15, 2019
Contact name Eric T Wang
Organization name University of Florida
Street address 2033 Mowry Rd
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
Platforms (2)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (6)
GSM581051 hnRNPH_CLIPSeq 1
GSM581052 hnRNPH_CLIPSeq 2
GSM582290 c2c12_lko_100
SRA SRP003495
BioProject PRJNA130865

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Supplementary file Size Download File type/resource
GSE23694_RAW.tar 1.1 Gb (http)(custom) TAR (of SAM)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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