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Series GSE58928 Query DataSets for GSE58928
Status Public on Jul 15, 2014
Title Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to compare transcriptomes using RNA-seq of mouse myoblasts (C2C12 cell line) in undifferentiated and differentiated states and with siRNA-mediated knock down of the RNA binding proteins, Rbfox1 (only expressed in differentiated state) and Rbfox2 (expressed in both undifferentiated and differentiated states).
Methods: Differentiated and undifferentiated C2C12 cultures treated with Rbfox1 (differentiated only) or Rbfox2 siRNAs or a mock siRNA transfection were used for RNA-Seq analysis using Illumina HiSeq2000. 101x2 paired-end RNA-seq reads were first uniquely aligned to the mouse genome (mm9) using TopHat 1.4.1. RSEM was used to count the number of reads mapped to genes using UCSC database, followed by edgeR to call differentially expressed genes with false discovery rate less than 0.01. Cufflinks was used to reconstruct isoforms and analyze alternative splicing and percent spliced in (PSI) was calculated. PSI values were validated by RT-PCR.
Results: 58-88% of the RNA-seq reads from technical and biological replicates mapped uniquely to the mouse genome. Analysis of gene expression and alternative splicing changes are published in Singh et al. Molecular Cell (2014).
Conclusions: Our study has identified gene expression and alternative splicing transitions that occur during myoblast differentiation, demonstrate that 30% of the splicing transitions are regulated by Rbfox2, demonstrated that Rbfox2 is required for a late step of myoblast differentiation and identified two Rbfox2-regulated splicing transitions that are required for differentiation.
Overall design Undifferentiated and differentiated C2C12 cultures with Rbfox2 depletion or Rbfox1 depletion (differentiated only) in at least duplicate samples analyzed by deep sequencing on Illumina HiSeq2000.
Contributor(s) Singh RK, Xia Z, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, Li W, Cooper TA
Citation(s) 25087874
Submission date Jun 30, 2014
Last update date May 15, 2019
Contact name Zheng Xia
Organization name Oregon Health & Science University
Department Department of Biomedical Engineering
Lab Xia Lab
Street address 3181 SW Sam Jackson Park Rd
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (11)
GSM1422390 Differentiated C2C12 Si-Control (Bio-rep1)
GSM1422391 Differentiated C2C12 Si-Control (Bio-rep2)
GSM1422392 Differentiated C2C12 Si-RbFox2 (Bio-rep1)
BioProject PRJNA253937
SRA SRP043682

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Supplementary file Size Download File type/resource
GSE58928_RAW.tar 3.4 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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