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Series GSE113253 Query DataSets for GSE113253
Status Public on Dec 01, 2018
Title Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Here we have used both chromatin accessibility and enhancer activity marks to study enhancer activation and changes in transcriptional networks during the differentiation of human MSC into osteoblasts and adipocytes. We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, while osteogenesis involves activation of pre-established enhancers. Using machine learning algorithms for in silico modeling of transcriptional regulation we predict the repertoire of transcription factors that drive the two differentiation pathways. We show that osteoblast differentiation depends on the activation of a large and diverse transcriptional network of pro-osteogenic and anti-adipogenic transcription factors. Intriguingly, knockdown of single members of this network is sufficient to modulate differentiation in both directions, indicating that lineage-determination is a delicate balance between activities of many different transcription factors.
Overall design Genome-wide profiling of chromatin accessibility and enhancer activity using H3K27ac and MED1 ChIP-seq during differentiation of human mesenchymal stem cells towards osteoblasts and adipocytes

Raw data are not available for primary stromal cell samples due to patient privacy concerns. If you are interested in accessing these data, please contact the submitter directly.
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Contributor(s) Rauch A, Haakonsson AK, Madsen JG, Larsen M, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S
Citation(s) 30833796
Submission date Apr 17, 2018
Last update date Mar 22, 2019
Contact name Susanne Mandrup
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (170)
GSM3100933 DNase-seq, BM-hMSC-TERT4 osteoblast diff 7d rep1
GSM3100934 DNase-seq, BM-hMSC-TERT4 osteoblast diff 7d rep2
GSM3100935 DNase-seq, BM-hMSC-TERT4 osteoblast diff 3d rep1
BioProject PRJNA450599
SRA SRP140638

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Supplementary file Size Download File type/resource
GSE113253_ATAC_HumanPrimaryStromalCells.bed.gz 887.2 Kb (ftp)(http) BED
GSE113253_ATAC_HumanPrimaryStromalCells.txt.gz 4.1 Mb (ftp)(http) TXT
GSE113253_ATAC_TERTimmortalizedCells.bed.gz 835.1 Kb (ftp)(http) BED
GSE113253_DNase_processed_data.tar.gz 32.8 Gb (ftp)(http) TAR
GSE113253_GeneExpr_AT.txt.gz 5.0 Mb (ftp)(http) TXT
GSE113253_GeneExpr_BM.txt.gz 5.5 Mb (ftp)(http) TXT
GSE113253_H3K27ac_ChIP-seq_processed_data.tar.gz 15.3 Gb (ftp)(http) TAR
GSE113253_MED1_ChIP-seq_processed_data.tar.gz 19.4 Gb (ftp)(http) TAR
GSE113253_RAW.tar 116.5 Mb (http)(custom) TAR (of ZIP)
GSE113253_RNA_HumanPrimaryStromalCells.txt.gz 4.9 Mb (ftp)(http) TXT
GSE113253_RNA_NonMesenchymalCells.txt.gz 4.7 Mb (ftp)(http) TXT
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Processed data are available on Series record

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