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Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [miR]

ABSTRACT: Here, we have focused on studying the link between metabolic changes driven by the differentiation into mature adipocytes of a human preadipocyte cell line (SGBS) and their regulation, through a combined experimental and computational approach. By collecting data on gene expression, PPARg, CEBPa, LXR and H3K4me3 genome-wide ChIP-seq profles and transcriptome-wide microRNA target identification for miR-27a, miR29a and miR-222, and using constraint-based modeling to estimate metabolic reaction activity, we obtained a comprehensive set of information highlighting how epigenetic, transcriptional and post-transcriptional regulation impacts the metabolic network. Illumina HT12 V4.0 microarrays: Transcriptome analysis 24 hours following overexpression of indicated microRNAs or control siRNAs on indicated time points of differentiation (D0 or D4 + 24 hours) (7 conditions in triplicate, total of 21 samples + siLamin transfection as positive control in duplicate) This submission represents transcriptome component of study.

ORGANISM(S): Homo sapiens

SUBMITTER: Merja Heinäniemi 

PROVIDER: E-GEOD-41576 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.

Galhardo Mafalda M   Sinkkonen Lasse L   Berninger Philipp P   Lin Jake J   Sauter Thomas T   Heinäniemi Merja M  

Nucleic acids research 20131105 3

Metabolic diseases and comorbidities represent an ever-growing epidemic where multiple cell types impact tissue homeostasis. Here, the link between the metabolic and gene regulatory networks was studied through experimental and computational analysis. Integrating gene regulation data with a human metabolic network prompted the establishment of an open-sourced web portal, IDARE (Integrated Data Nodes of Regulation), for visualizing various gene-related data in context of metabolic pathways. Motiv  ...[more]

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