Chromatin immunoprecipitations were performed as previously described (Bhandare et al., 2010). Briefly, samples were crosslinked in 1.1% formaldehyde/PBS for 15 min at room temperature and then quenched with 0.125M glycine/PBS. Samples were subsequently washed twice with PBS and then lysed in 1% SDS. For sonication, lysates were sonicated with a Bioruptor Sonicator (Diagenode) six times for 5 min each with a 30 sec on and off cycle, resulting in 200-500bp chromatin fragments. Sheared chromatin was incubated overnight at 4 °C with 5 µg rabbit anti-SOX9 antibody (Millipore, AB5535; Lot number 2262679). Chromatin and antibody complex was incubated with 12.5 µl of Dynabeads protein A plus 12.5 µl of Dynabeads protein G (Life Technologies) at 4 °C for 4 hrs. Immunoprecipitated complexes were further eluted, reverse crosslinked, and subjected to library preparation. ChIP-seq libraries were prepared as per Illumina’s instructions (http://www.illumina.com). For input library preparation, 50 ng of input DNA from each sample was used. After adaptor ligation, DNA fragments were size-fractionated by gel electrophoresis and excised at 200±25 bp. Following gel purification, DNA fragments were amplified with 18 PCR cycles and purified using a MiniElute PCR Purification kit (Qiagen). 10 nM purified DNA was loaded on the flow cell, and sequencing was performed on an Illumina/Solexa Genome Analyzer II in accordance with the manufacturer’s protocols.