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Series GSE16992 Query DataSets for GSE16992
Status Public on Mar 21, 2012
Title Expression Profiling of Early Myogenesis - Affymetrix Dataset
Organism Mus musculus
Experiment type Expression profiling by array
Summary Analysis of Early Myogenesis Reveals an Extensive Set of Transcriptional Regulators Whose Knock-down Can Inhibit Differentiation
Myogenesis is a tightly controlled process involving the transcriptional activation and repression of thousands of genes. Although many components of the transcriptional network are known for the later phases of myogenesis, relatively little work has described the transcriptional landscape within the first 24 hours, when myoblasts commit to differentiate. Through dense temporal sampling of differentiating C2C12 myoblasts, we identify 266 transcriptional regulators (TRs) whose expression is altered within the first 12 hours of myogenesis. A high-content shRNA screen of 76 TRs involving 427 stable lines identified 48 genes whose knockdown significantly inhibits differentiation of C2C12 myoblasts. These include known regulators of myogenesis (Myod1, Myog and Myf5), as well as 26 regulators not previously associated with the process. Of the TRs differentially expressed within the first 24 hours, two-thirds inhibited differentiation when knocked down. Surprisingly, a similar proportion (67%) of shRNAs targeting TRs whose expression did not change during differentiation also inhibited myogenesis, suggesting that both stably and differentially expressed TRs are essential for this complex differentiation program. This implies that microarray-based approaches that concentrate functional validation studies on differentially-expressed genes will fail to identify many genes that are critically implicated in complex biological processes.
Overall design C2C12 myoblasts were differentiated into myotubes and sampled at various timepoints for gene expression measurement on MOE-430v2 chips. Cells grown in separate plates were harvested at 14 different timepoints: t_-24h, t_0h, t_0.5h, t_1h, t_1.5h, t_2h, t_3h, t_6h, t_9h, t_12h, t_24h, t_48h, t_96h, t_144h. Cells were also pre-treated with 50uM cycloheximide 1 hour prior to inducing differentiation and harvested at two timepoints: t_chx_1h, t_chx_3h. All harvests were performed in triplicate using growths from successive passages.
Contributor(s) Sundararajan S, Sladek R, Hudson TJ
Citation(s) 22147266
Submission date Jul 08, 2009
Last update date Feb 11, 2019
Contact name Saravanan Sundararajan
Organization name McGill University
Department Human Genetics
Lab Rob Sladek
Street address 740, Dr Penfield Ave
City Montreal
State/province Quebec
ZIP/Postal code H3A 1A4
Country Canada
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (48)
GSM425337 C2C12_-24hr_ctrl_rep1
GSM425338 C2C12_-24hr_ctrl_rep2
GSM425339 C2C12_-24hr_ctrl_rep3
This SubSeries is part of SuperSeries:
GSE17039 Expression Profiling of Early Myogenesis
BioProject PRJNA122679

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
GSE16992_RAW.tar 280.3 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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