title: GSM1181852: Runx3_CD4DC_CHIP_Runx3_IP2; Mus musculus; ChIP-Seq
library_construction_protocol: Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 40ul of anti-Runx3 Ab were added to 15 mL of diluted, fragmented chromatin; whole cell extract fragmented chromatin served as control. DNA was purified using QIAquick spin columns (QIAGEN). For ChIP-seq analysis, indexed CiHP-seq libraries were prepared as published Blecher-Gonen et al. Nature Protocols 8, 539–554 (2013).  Illumina sequencing of short reads (50 bp) was performed in one lane of Hiseq 2000 using v3 clustering and sequencing reagents.