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Series GSE69110 Query DataSets for GSE69110
Status Public on Jul 01, 2015
Title Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly through a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis.
Overall design Incorportation of ChIP-seq data of Sox9 and histone modification marks for chromatin status together with micorarray gene expression profiling in neonatal mice chondrocytes to uncover Sox9 regulatory system. Overexpression of Sox9 with a control of EGFP in human fibroblasts to identify the direct targets of Sox9 regulatory system
Contributor(s) He X, Ohba S, Hojo H, McMahon AP
Citation(s) 26146088
Submission date May 21, 2015
Last update date May 15, 2019
Contact name Xinjun He
Phone 323-442-8077
Organization name University of Southern California
Department BROAD CIRM Center
Street address 1425 San Pablo St
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM1693009 Ad-eGFP-RNAseq_1
GSM1693010 Ad-eGFP-RNAseq_2
GSM1693011 Ad-eGFP-RNAseq_3
This SubSeries is part of SuperSeries:
GSE69111 Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte
BioProject PRJNA284582
SRA SRP058567

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Supplementary file Size Download File type/resource
GSE69110_d2GFP_vs_d2Sox9OE.deseq.counts.csv.gz 268.0 Kb (ftp)(http) CSV
GSE69110_d2GFP_vs_d2Sox9OE.deseq.res.csv.gz 564.8 Kb (ftp)(http) CSV
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Processed data are available on Series record

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