Published October 1, 2019 | Version 3.0
Dataset Open

Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism

Description

This dataset is a complement to the following publication: Ahmed M. Abdelmoez, Laura Sardón Puig, Jonathon AB. Smith, Brendan M. Gabriel, Mladen Savikj, Lucile Dollet, Alexander V. Chibalin, Anna Krook, Juleen R. Zierath, and Nicolas J. Pillon. Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism. Am J Physiol Cell Physiol. 2019 Dec 11.

METHODS: Publicly available data from myotubes and skeletal muscle tissues were selected from the GEO database. Raw files were downloaded and robust multi array (RMA) normalization was performed in unison for all samples from the same platform. For each human ENSEMBL, the rat and mouse orthologs were found using the R package BioMart and the arrays were merged based on the human ENSEMBL annotation. The database was then aggregated according to the official human gene symbol. When multiple ENSEMBL were found for a single gene symbol, an average was calculated.

Notes

The authors are supported by grants from the Novo Nordisk Foundation (NNF14OC0011493, NNF17OC0030088 and NNF14OC0009941), Swedish Diabetes Foundation (DIA 2018-357, DIA2018-336), Swedish Research Council (2015-00165, 2018-02389), the Strategic Research Program in Diabetes at Karolinska Institutet (2009-1068), the Stockholm County Council (SLL20170159), the Swedish Research Council for Sport Science (P2018-0097) and the EFSD European Research Programme on New Targets for Type 2 Diabetes supported by an educational research grant from MSD. LD was supported by a Novo Nordisk postdoctoral fellowship run in partnership with Karolinska Institutet. BMG was supported by a fellowship from the Wenner-Gren Foundation (Sweden). NJP and LSP were supported by the Marie Skłodowska-Curie Actions (European Commission, 704978, 675610) and grants from the Sigurd och Elsa Goljes Minne and Lars Hiertas Minne Foundations (Sweden). We acknowledge the Beta Cell in-vivo Imaging/ Extracellular Flux Analysis core facility supported by the Strategic Research Program (SRP) in Diabetes for the usage of the Seahorse flux analyzer.

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Additional details

Funding

European Commission
ChroMe - Chromatin and Metabolism Chromatin-metabolism interactions as targets for healthy living 675610
European Commission
SMILED - Skeletal Muscle Inflammation: ambivalent roles in Exercise and Diabetes 704978

References