Cells were freshly isolated, fixed and frozen at -80°C.
strain
ICR
chip antibody
Runx3 poly clonal home made
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~200bp. For immunoprecipitation, 48ul of anti-Runx3 Ab 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 HiSeq2000 platform according to the manufactures instructions by loading 9 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (50 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).