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Series GSE41629 Query DataSets for GSE41629
Status Public on Nov 19, 2013
Title Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Heinäniemi M, Galhardo M, Sinkkonen L, Sauter T
Citation(s) 24198249
Submission date Oct 16, 2012
Last update date May 15, 2019
Contact name Merja Heinäniemi
Organization name university of eastern finland
Street address Yliopistonranta 1
City Kuopio
ZIP/Postal code 70210
Country Finland
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (6)
GSM1020361 preadipocyte_H3K4me3_ChIP-seq
GSM1020362 adipocyte_H3K4me3_ChIP-seq
GSM1020363 adipocyte_PPARg_ChIP-seq
This SubSeries is part of SuperSeries:
GSE41578 Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation
BioProject PRJNA177774
SRA SRP016497

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Supplementary file Size Download File type/resource
GSE41629_RAW.tar 175.7 Mb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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