Input normalized ChIP-seq and ChIP-chip fold enrichment profiles

ChIP-seq

To enable the cross-species comparisons described in this paper, we have reprocessed all data using MACS. (Due to the slight differences in the peak-calling and input normalization steps, there may be slight discrepancies between the fly profiles analyzed here and profiles available at the modENCODE data portal or modMine.

For every pair of aligned ChIP and matching input-DNA data, we used MACS version 2 to generate fold enrichment signal tracks for every position in a genome:
macs2 callpeak -t ChIP.bam -c Input.bam -B --nomodel --shiftsize 73 --SPMR -g hs -n ChIP
macs2 bdgcmp -t ChIP_treat_pileup.bdg -c ChIP_control_lambda.bdg -o ChIP_FE.bedgraph -m FE

ChIP-chip

For the fly data, genomic DNA Tiling Arrays v2.0 (Affymetrix) were used to hybridize ChIP and input DNA. We obtained the log-intensity ratio values (M-values) for all perfect match (PM) probes: M = log2(ChIP intensity) - log2(input intensity), and performed a whole-genome baseline shift so that the mean of M in each microarray is equal to 0. The smoothed log intensity ratios were calculated using LOWESS with a smoothing span corresponding to 500 bp, combining normalized data from two replicate experiments. For the worm data, a custom Nimblegen two-channel whole genome microarray platform was used to hybridize both ChIP and input DNA. MA2C was used to preprocess the data to obtain a normalized and median centered log2 ratio for each probe. All data are publicly accessible through the modENCODE data portal or modMine.
The input normalized profiles are availabe at ENCODE-X browser.

DNase-seq data

Aligned DNase-seq data were downloaded from the modENCODE data portal and the ENCODE UCSC download page. Additional Drosophila embryo DNase-seq data were downloaded. After confirming consistency, reads from biological replicates were merged. We calculated minimally-smoothed signals (by a Gaussian kernel smoother with bandwidth of 10 bp in fly and 50 bp in human) along the genome in 10 bp (fly) or 50 bp (human) non-overlapping bins.

MNase-seq data

The MNase-seq data were analyzed as described previously38. In brief, tags were mapped to the corresponding reference genome assemblies. The positions at which the number of mapped tags had a Z-score > 7 were considered anomalous due to potential amplification bias. The tags mapped to such positions were discarded. To compute profiles of nucleosomal frequency around TSS, the centers of the fragments were used in the case of paired-end data. In the case of single-end data, tag positions were shifted by the half of the estimated fragment size (estimated using cross-correlation analysis39 toward the fragment 3’-ends and tags mapping to positive and negative DNA strands were combined). Loess smoothing in the 11-bp window, which does not affect positions of the major minima and maxima on the plots, was applied to reduce the highfrequency noise in the profiles.