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Series GSE54631 Query DataSets for GSE54631
Status Public on Jul 29, 2014
Title Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions using RNA-Seq Data
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We developed a bioinformatics approach called the Read-Split-Walk (RSW) pipeline, and evaluated it using two Ire1α heterozygous and two Ire1α-null samples. The 26nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1α knockout samples. We compared the Xbp1 results from our approach with results using the alignment program BWA, STAR, Exonerate and the Unix “grep” command. We then applied our RSW pipeline to RNA-Seq data from the SKBR3 human breast cancer cell line. RSW reported a large number of non-canonical spliced regions for 108 genes in chromosome 17, which were identified by an independent study.
Overall design Identification of non-canonical spliced regions for mouse MEF samples (two Ire1α heterozygous and two Ire1α-null samples)
Contributor(s) Bai Y, Hassler J, Kaufman RJ, Sartor MA
Citation(s) 24991935
Submission date Feb 03, 2014
Last update date May 15, 2019
Contact name Maureen Sartor
Organization name University of Michigan
Street address 100 Washtenaw Avenue
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1320292 KO_Tg_untreated
GSM1320293 Het_Tg_treated
GSM1320294 KO_Dtt_untreated
BioProject PRJNA237229
SRA SRP036157

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54631_Dtt_RSW_processed.txt.gz 44.5 Kb (ftp)(http) TXT
GSE54631_Tg_RSW_processed.txt.gz 1.3 Kb (ftp)(http) TXT
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Processed data are available on Series record

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