BroadPeak

[…] stem cell-derived neurons were generated by the epigenomics roadmap. preprocessed broad peak calls for h3k4me3 were downloaded from http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/. peaks with a negative log10 p-value of 5 or greater were retained for further analysis, as described in the original macs protocol., h3k4me3 chip-sequencing data from neun-positive […]

[…] data availability: , data generated by the roadmap epigenomics project were downloaded from http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/dnase/, http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/broadpeak/ , http://egg2.wustl.edu/roadmap/data/byfiletype/peaks/consolidated/narrowpeak/ , blueprint monocyte […]

[…] to improve disease risk prediction performance []., we used tissue-specific snp annotations from the encode [] and the roadmap [] projects in the present study. specifically, we downloaded the broadpeak files from the roadmap epigenomics web portal (http://egg2.wustl.edu/roadmap/web_portal/). the broadpeak files contain peak regions for four histone marks (h3k27me3, h3k36me3, h3k4me1, […]

[…] parameters), and (2) broader regions of enrichment (broadpeaks) that pass a q-value threshold of 0.05 (broad peak mode of macs v2.1.0). for the broad-range histone marker, h3k27me3, we used the broadpeak representation of macs v2.1.0 peak caller., we designed four different guide rnas (grnas) targeting a 20-bp site (protospacer) in the human cdh1 locus that precedes an ngg trinucleotides, […]

[…] transcriptional target genes were predicted from promoter (additional file : figure s7)., ctcf chip-seq data for monocytes cd14+ cells (gsm1003508_hg19_wgencodebroadhistonemonocd14ro1746ctcfpk.broadpeak.gz), cd4+ t cells (srr001460.bam), cd20+ b cells (gsm1003474_hg19_wgencodebroadhistonecd20ctcfpk.broadpeak.gz), h1-hesc (wgencodeawgtfbsutah1hescctcfunipk.narrowpeak.gz), ipsc (gse96477), […]

[…] (version 0.1.19)(). properly-paired reads only were selected for further analysis., chip and input reads from each individual were used to call peaks in each individual using macs2 () with the broadpeak option at various qvalue cut-offs. a lenient threshold of qvalue = 0.1 was used in subsequent analysis to maximize the number of regions identified in each species., to determine […]