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Series GSE60237 Query DataSets for GSE60237
Status Public on Dec 10, 2014
Title A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Adipose stem cells (ASCs) and adipocytes play a crucial role in maintaining energy balance. We aim to examine the temporal relationship between gene expression and histone modification transitions during in vitro differentiation of human ASCs into adipocytes. Here, we examine by RNAseq proliferating ASCs (Day -2 prior to adipogenic induction), confluent ASCs (Day 0, adipogenic induction), pre-adipocytes (Day 3) and maturing adipocytes (Day 9). We find 1060, 5452 and 2216 genes differentially expressed between D-2/D0, D0/D3 and D3/D9 respectively. We identify gene clusters with distinct and dynamic expression patterns. In particular, adipogenic induction is marked by temporal waves of gene induction and downregulation. We report two types of transcriptional waves: (i) those showing transient induction or inactivation at D0, D3 or D9, and involved in sensory perception and immune response functions; and (ii) those showing long-lived induction or repression at these time points. Our data reveal a dynamic network of gene regulation during adipogenesis, involving signaling, immune and developmental processes. We identify 15 unique epigenetic states using Hidden Markov Modeling which reflects an epigenetically highly organised genome showing enhancer states are commonly consecutive. A heatmap for the abundance of epigenetic states for the expression clusters reveals a link between expression and epigenetic marking of the state suggesting an increase in the number of number of chromatin states with increase in expression. Our data point to a model of increased epigenetic complexity associated with gene expression.
Overall design Examination of expression of profiles of ASCs across differentiation
Contributor(s) Shah A, Oldenburg A, Collas P
Citation(s) 25551786
Submission date Aug 08, 2014
Last update date May 15, 2019
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1468492 ASC_Day-2
GSM1468493 ASC_Day0
GSM1468494 ASC_Day3
BioProject PRJNA257805
SRA SRP045364

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Supplementary file Size Download File type/resource
GSE60237_RAW.tar 650.0 Kb (http)(custom) TAR (of CSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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