DRIP-seq experiment on human Jurkat cells (INPUT; Rep2)
Briefly, cells were cross-linked with 1% paraformaldehyde (10 min). Cells were lysed and total nucleic acids were extracted and purified using NucleoSpin Tissue Kit (Macherey-Nagel). DNA was fragmented with sonication (30 sec ON, 30 sec OFF, LOW, Bioruptor) to yield an average DNA fragment size of ~500 bp. After fragmentation fragment analysis was done by using 1 % agarose gelelectophoreses. If it was necessary, further sonication was applied. Fragmented samples were purified (2% is kept for input DNA) and immunoprecipitated with S9.6 antibody overnight. After elution, purified immunprecipitated DNA was used to create sequencing library using Illumina's TruSeq ChIP Sample Preparation protocol.