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Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE41578 | GEO | 2013/11/19

SECONDARY ACCESSION(S): PRJNA177563

REPOSITORIES: GEO

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Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-19 | E-GEOD-41578 | biostudies-arrayexpress

Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [T0901317]

Project description: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 V3.0 microarrays: LXR ligand activation with 1 microM T0901317 for 4 h in SGBS day 10 differentiated adipocytes (6 samples, treatment vs control, in triplicate) This submission represents transcriptome component of study.

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

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

Project description: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 microarrays: Time series of differentiation (20 samples, 7 time points in duplicate or triplicate) This is the Illumina Gene Expression part of the study.

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Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [ChIP-Seq]

Project description: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 Solexa sequencing: Six samples in total. Two ChIP-seq samples were prepared using an antibody against H3K4me3 active TSS chromatin marker from human SGBS preadipocyte and day 10 differentiated SGBS adipocyte cells. From day 10 differentiated SGBS cells additional three samples were prepared using an antibody against PPARg, CEBPa and LXRa to determine their genome-wide binding. One input control sample is included.

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