Similar protocols

Pipeline publication

[…] ChIP–seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Briefly, each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 200–300 bp. After DNA clean up, samples were amplified with 13 (H3) or 19 (BAZ1A and SMARCA5) cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length., ChIP–seq data were aligned to the mouse genome (mm9) by CASAVA 1.8 (, and only unique reads were retained for analysis. FastQC ( was applied for quality control, and then SAMTools ( was used to remove potential PCR duplicates. PhantomPeak ( was applied to estimate the quality and enrichment of the ChIP–seq dataset. Additional ENCODE quality metrics, such as the normalized strand coefficient (NSC) and the relative strand correlation (RSC), were calculated. For all samples in our research, NSC≥1.05, RSC≥0.8. Basic filtering and quality control confirmed that these samples were of strong quality and exceeded ENCODE standards; see and (raw and genome–browser compatible files can be accessed online at For the H3 MNase ChIP–seq libraries, 150+ million raw reads were obtained for each replicate. With ~70% reads uniquely mapp […]

Pipeline specifications

Software tools BCL2FASTQ Conversion Software, FastQC, SAMtools, phantompeakqualtools
Organisms Mus musculus, Homo sapiens
Chemicals Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides