4 protocols
normalization data transformation protocol
ChIP-Seq reads were aligned to genome build hg18 and filtered by removing reads either with quality less than 5 or overlapping signal artefact regions (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/). Peaks were called using model-based analysis for ChIP-Seq (MACS) (Zhang et al., Genome Biology, 9(9):R137, 2008), run using default parameters. Quality control of the raw sequenced data was conducted using the FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and good quality scores across all bases were observed. To evaluate the consistency of signal between replicates we measured the read coverage over all genomic regions covering peak regions that were called in at least two of the three replicates. There is a good correlation between pairs of replicates, with Spearman’s correlation coefficients ranging from 0.51 to 0.74 Genome_build: hg18 Supplementary_files_format_and_content: Files produced by MACS that report peak positons, summit and statistics. The files named NAME_peaks.bed are in BED format which contains the peak locations and in the 5th column is the -10*log10pvalue of peak region. The files names NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks, and in the 5th column in this file is the summit height of fragment pileup.
growth protocol
MCF7 cells were grown in DMEM supplemented with 10% heat-inactivated foetal calf serum and 1% penicillin-streptomycin.
sample treatment protocol
Cells growing asynchronously in full media were fixed for ChIP.
nucleic acid library construction protocol
ChIP of DNA was performed as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001 Illumina sequencing libraries were prepared as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001