Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: For ChIP-seq: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 min RT. Pelleted cells were lysed in Lysis buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40, plus protease inhibitors and 0.5 mM DTT), incubated on ice for 10 minutes and centrifuged at 8000xg 10 min to pellet the nuclei. Nuclei were resuspended in Lysis buffer II (1%SDS, 10 mM EDTA, 50 mM tris ClH pH 8.1 plus protease inhibitors), incubated on ice for 10 min and sonicated for 15 min (15 cycles, each one 30sec “on”, 30 sec “off”) in a Bioruptor (Diagenode, Seraing, Belgium) in order to generate 200bp fragments. For ChIP-seq: Libraries of immunoprecipitated and input DNA were prepared using the NEBNext DNA sample prep reagent Set 1 kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol. For ATAC-seq: Fresh nuclei were obtained using Lysis Buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40) For ATAC: Fresh nuclei incubated 30min at 37ºC with Tn5 transposases from the Nextera DNA Library Prep Kit (Illumina, San Diego, CA)