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Series GSE38497 Query DataSets for GSE38497
Status Public on Aug 16, 2012
Title Muscleblind-Like 2 mediated alternative splicing in the developing bain by mRNA sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We have identified Mbnl2 mediated splicing events and mRNA expression regulation by comparing WT and Mbnl2 ΔE2/ΔE2 mouse hippocampii using Affymetrix Mouse Exon Junction Array and mRNA sequencing.

The splicing microarray data has already been submitted under GSE37908 which also includes a re-analysis of RNA-seq data.

The TableS1.xls contains Splicing microarray analysis data of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus.
The TableS2.xls files contain RNA-Seq, Gene Ontology, HITS-CLIP and CIMS summary of Mbnl2+/+ vs. MBNL2 ΔE2/ΔE2 knockout hippocampus.
The file contents are descibed in the 'TableS1_S2_readme.pdf' and data processing details are included in the 'data_processing_readme.pdf' file.

The Mbnl2_TableS2.xls contains data from exon junction microarrays for splicing analysis between WT and Mbnl2 delta2 mice. It also contains RNA-seq based splicing analysis between WT and Mbnl2 delta2 mice. Mbnl2_TableS2 further contains common targets between the two analyses, Gene Ontology and finally the HITS-CLIP data. CLIP tag summary describes read numbers for the three biological replicates. CLIP sig peaks contains significant HITS-CLIP unique reads/peaks after processing the data (BED files). Finally, CIMS analysis describes the Mbnl2 binding motif.
Overall design 9 total samples were analyzed; 6 for RNA-seq: brains from 3 WT and 3 MBNL2 E2/ E2 female mice, all 2-3 months of age, and 3 for HITS-CLIP: brains from 3 WT BL6 female mice, all 2-3 months of age.
Contributor(s) Ranjan B, Chaolin Z
Citation(s) 22884328
Submission date Jun 05, 2012
Last update date May 15, 2019
Contact name Ranjan Batra
Phone 352-222-9209
Organization name University of California San Diego
Department Cellular and Molecular Medicine
Lab Yeo Lab
Street address 2880 Torrey Pines Scenic Drive
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (9)
GSM943590 WT, biological rep1
GSM943591 WT, biological rep2
GSM943592 WT, biological rep3
BioProject PRJNA168021
SRA SRP013558

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
GSE38497_Mbnl2_TableS2.xls.gz 727.5 Kb (ftp)(http) XLS
GSE38497_RAW.tar 459.6 Mb (http)(custom) TAR (of BED, BEDGRAPH)
GSE38497_TableS1.xls.gz 71.2 Kb (ftp)(http) XLS
GSE38497_TableS1_S2_readme.pdf 158.7 Kb (ftp)(http) PDF
GSE38497_TableS2.xls.gz 59.1 Kb (ftp)(http) XLS
GSE38497_data_processing_readme.pdf 124.7 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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