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Series GSE129025 Query DataSets for GSE129025
Status Public on Mar 31, 2020
Title A chondrocyte-specific Indian hedgehog enhancer activated in both skeletal development and postnatal cartilage degeneration [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Sox6-DNA interaction was profiled in the same chondrocyte population as used for our Sox9 ChIP-seq analysis (GSE69109). First, we classified Sox6 peaks into TSS-associated Class I and distally located Class II as in our previous study. Class II targets were strongly associated with genes related to skeletal tissues, whereas Class I targets were related to general cellular processes, not chondrocyte-specific activities. When we investigated the overlap of the Sox6 ChIP-seq peaks with Sox9 ChIP-seq peaks identified in our previous study, the majority of Sox9 peaks overlapped with Sox6 peaks in both Class I and Class II regions, which is in line with previous findings that Sox9 and Sox6 co-engage in gene expression for the chondrocyte program.
 
Overall design Sox6 ChIP-seq in mouse primary rib chondrocytes.
Sox9 ChIP-seq in mouse primary rib chondrocytes: Third-party re-analysis of Samples GSM1692996 and GSM1693004. Peak calling of Sox9 was performed as for Sox6. Processed data file Cho_Sox9.2s.FDR1.peaks.bed.gz linked below as a supplementary file.
 
Contributor(s) Yamakawa A, Hojo H, Ohba S
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Submission date Mar 29, 2019
Last update date Apr 02, 2020
Contact name Shinsuke Ohba
E-mail(s) shinohba-tky@umin.ac.jp
Organization name The University of Tokyo
Department Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine
Lab Ohba-Tei/Chung Lab
Street address 7-3-1 Hongo, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8655
Country Japan
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (2)
GSM3690889 Sox6_ChIP-Seq
GSM3690890 Input DNA
Relations
Reanalysis of GSM1692996
Reanalysis of GSM1693004
BioProject PRJNA529793
SRA SRP189845

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129025_Cho_Sox9.2s.FDR1.peaks.bed.gz 220.9 Kb (ftp)(http) BED
GSE129025_RAW.tar 730.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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