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Series GSE63154 Query DataSets for GSE63154
Status Public on Nov 11, 2014
Title Gene co-expression network analysis of myostatin regulation at three different mouse developmental timepoints
Organism Mus musculus
Experiment type Expression profiling by array
Summary Myostatin (Mstn) knockout mice exhibit large increases in skeletal muscle mass. However, relatively few of the genes that mediate or modify MSTN effects are known. In this study, we performed co-expression network analysis using whole transcriptome microarray data from Mstn-null and wild-type mice to identify genes involved in important biological processes and pathways related to skeletal muscle and adipose development.Genes differentially expressed between wild-type and Mstn-null mice were identified at 13.5 d.p.c. and 35 days after birth (d35) and further analyzed for shared DNA motifs using DREME.
Known and novel transcription factor binding sites involved in MSTN signal transduction were enriched in differentially expressed genes. The use of regulatory impact factor (RIF), phenotypic impact factor (PIF), and differential hubbing analyses with the partical correlation and information theory (PCIT) co-expression analysis methods identified both known and potentially novel regulators of muscle development. These results provide new details of how MSTN may mediate transcriptional regulation as well as insight into novel regulators of MSTN signal transduction that merit further study regarding their physiological roles in muscle and adipose development.
 
Overall design Mstn-null and wild-type mice were reared, sacrificed by CO2 asphyxiation (embryonic timepoints) or cervical dislocation (d35), and tissues were collected from whole embryos (13.5 d.p.c.), hindquarters (17.5 d.p.c.), or pectoralis muscle (d35). After collection, muscles were flash-frozen in liquid nitrogen as previously described in Steelman et al., 2006. FASEB J. Mar;20(3):580-2. For microarray analysis, 10 μg of RNA from each of three individual animals was pooled to give five pools (N=15, total number of arrays=5) for each genotype/timepoint combination.
 
Contributor(s) Yang X, Koltes JE, Park CA, Chen D, Reecy JM
Citation(s) 25695797
Submission date Nov 10, 2014
Last update date Aug 16, 2019
Contact name James M Reecy
Organization name Iowa State University
Department Animal Science
Lab Reecy Lab
Street address 2255 Kildee Hall, Iowa State University
City Ames
State/province IA
ZIP/Postal code 50011-3150
Country USA
 
Platforms (2)
GPL339 [MOE430A] Affymetrix Mouse Expression 430A Array
GPL340 [MOE430B] Affymetrix Mouse Expression 430B Array
Samples (60)
GSM1542274 Mstn-null sample at 13.5 d.p.c, biological rep1 (MOE430A)
GSM1542275 Mstn-null sample at 13.5 d.p.c, biological rep2 (MOE430A)
GSM1542276 Mstn-null sample at 13.5 d.p.c, biological rep3 (MOE430A)
Relations
BioProject PRJNA266824

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
GSE63154_RAW.tar 124.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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