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Series GSE63887 Query DataSets for GSE63887
Status Public on Apr 07, 2015
Title RNA-sequencing of healthy human skeletal myocytes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Skeletal myocytes are metabolically active and susceptible to insulin resistance, thus implicated in type 2 diabetes (T2D). This complex disease involves systemic metabolic changes and their elucidation at the systems level requires genome-wide data and biological networks. Genome-scale metabolic models (GEMs) provide a network-context to integrate high-throughput data. We generated myocyte-specific RNA-seq data and investigated their correlation with proteome data. These data were then used to reconstruct a comprehensive myocyte GEM. Next, we performed a meta-analysis of six studies comparing muscle transcription in T2D versus healthy subjects. Transcriptional changes were mapped on the myocyte GEM, revealing extensive transcriptional regulation in T2D, particularly around pyruvate oxidation, branched-chain amino acid catabolism, and tetrahydrofolate metabolism, connected through the down-regulated dihydrolipoamide dehydrogenase. Strikingly, the gene signature underlying this metabolic regulation successfully classifies the disease state of individual samples, suggesting that regulation of these pathways is a ubiquitous feature of myocytes in response to T2D.
Overall design Isolated skeletal muscle precursor cells from six normal glucose tolerant and non-obese males and females were differentiated in vitro. RNA from fully differentiated myotubes was sequenced using RNA-seq.
Contributor(s) Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Klarlund Pedersen B, Nielsen J
Citation(s) 25937284, 28545587
Submission date Dec 05, 2014
Last update date May 15, 2019
Contact name Leif Väremo
Organization name Chalmers University of Technology
Department Biology and Biological Engineering
Street address Kemivägen 10
City Gothenburg
ZIP/Postal code 41296
Country Sweden
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM1559439 Male1_34a_non-obese_ngt_0h
GSM1559440 Male2_32a_non-obese_ngt_0h
GSM1559441 Male3_35a_non-obese_ngt_0h
BioProject PRJNA269336
SRA SRP050596

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63887_FPKM-values.txt.gz 848.5 Kb (ftp)(http) TXT
GSE63887_RAW.tar 1.3 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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