P-GSE12680-5 - P-GSE12680-5
Images analysis and base calling was done using solexa pipeline and reads aligned to both mouse NCBI build 36 using ELAND. For ChIP-Seq, sequences from all lanes were extended 200bp (maximum fragment length accounting for ~100bp of primer sequence), and allocated into 25 bp bins. Genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9. Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) from matched cell samples (>5X normalized enrichment across the entire region).