Chromatin immunoprecipitation was carried out as described previously with minor modifications (Saladi et al., 2017). Briefly, cells were cross-linked with 2 mM EGS (Ethylene Glycol-bis (Succinimidylsuccinate)) in PBS for 30 minutes at room temperature followed by cross-linking with 1% (v/v) formaldehyde at room temperature for 15 minutes. 125 mM glycine was added to stop cross-linking. Cells were then lysed in RIPA buffer for 1-2 hr at 40C. Nuclear lysates were sonicated 5 min for 8 times in a Bioruptor (Diagenode). Sonicated chromatin was precleared with Protein G Sepharose beads (GE Healthcare) pre-blocked with BSA and sonicated salmon sperm DNA (15632-011, Invitrogen). Samples were incubated with 2μg antibody (SOX2, IgG) for overnight at 40C followed by incubation with beads for additional 4 hrs. Immunoprecipitated beads were washed in wash buffer 1 (containing 150 mM NaCl), wash buffer 2 (containing 500 mM NaCl), wash buffer 3 (containing 250 mM LiCl). After the wash, beads were incubated for 3 hrs at 550C, then overnight at 650C in TE buffer containing, SDS, RNase A, and Proteinase K. DNA was purified via Qiaquick PCR purification kit (28106, Qiagen) as per manufacturer's instructions. PCR was performed using IQ SYBR Green Supermix reagent (Bio-Rad) in a MX300P machine (Stratagene). Percentage of input from the IPs was calculated by using 10% as standard. Libraries were preparation using the NEBNext Ultra DNA Library Prep Kit with manufacturer's instructions. 11 cycles were used for the library amplification. Compatible barcodes #1-12 from Illumina were used. Single end 50bp sequencing was done on HiSeq 2000 using TruSeq V3 High-output kits.