A chondrocyte-specific Indian hedgehog enhancer activated in both skeletal development and postnatal cartilage degeneration [ChIP-seq]

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. 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.