Instrument: Illumina Genome Analyzer IIx
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Cultured NK cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN). For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).