GSM1407357: Input_WT; Mus musculus; ChIP-Seq
Sonicated nuclei were cleared by centrifugation and incubated overnight with anti-Zfp335 bound to Dynabeads. Beads were washed in low-salt buffer, high-salt buffer, LiCl buffer and TE buffer. Protein/DNA complexes were eluted, reverse-crosslinked overnight at 65°C and treated with RNase A and proteinase K. ChIP DNA was purified using QIAquick PCR Purification kit (Qiagen). 7-10 ng ChIP DNA and 10 ng input DNA were used for library preparation, performed according to Illumina's TruSeq protocol with some modifications. DNA clean-up, removal of adapter dimers and size selection (300-500 bp) were done using Agencourt AMPure XP beads (Beckman Coulter). Libraries were checked for quality using the High Sensitivity DNA Bioanalyzer kit (Agilent Technologies), quantified with the Qubit dsDNA HS Assay kit (Life Technologies), and sequenced as 50 bp single-end reads on the Illumina HiSeq 2000 platform.