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Pipeline publication

[…] After RNase A and proteinase K digestion, DNA was purified and cloned in a barcoded sequencing library for the Illumina sequencing platform. In brief, after DNA repair and A-addition NEBNext adapters (NEB, E7335) were ligated and digested with the USER enzyme. Barcodes (NEB, E7335) were introduced via PCR with a maximum of 14 cycles by the NEBNext polymerase (NEB, M0541). Size selection for mononucleosomal insert fragments was done with Ampure XP beads (Agencourt, A63880). Each ChIP-seq library was sequenced on the Illumina HiSeq 2000 with 50bp single-end in 2 replicates, whereas the H3-chip samples were sequenced with 50 bp paired-ends in 2 replicates., H3 ChIP-seq reads were mapped using Bowtie allowing up to 1 mismatch and counting only unique hits, obtaining the following number of mapped 100-bp paired-end reads: 248 million for undifferentiated HL-60/S4 cells, 319 million for RA-treated HL-60/S4, and 338 million reads for TPA-treated HL-60/S4. The average DNA fragments lengths were correspondingly 160 bp, 159 bp and 159 bp, reflecting a moderate chromatin digestion (in a strongly digested chromatin DNA fragments are closer to the 147bp nucleosome DNA length). Mapped reads were processed using NucTools to generate genome-wide nucleosome occupancy landscapes, extract individual genomic regions and calculate NRL, as described previously. Aggregate nucleosome occupancy profiles around genomic features were calculated using HOMER and visualized using OriginPro 2016 (OriginLab Corporation). For the analysis performed in this manuscripts, we used the corresponding RefSeq definitions of promoters (extended +/−1,000 from TSS), FANTOM definitions of enhancers and Dfam definitions of ALU repeats. The coordinates of transcription factor binding sites and DNaseI-sensitive regions in HL-60 cells determined by the ENCODE consortium were obtained from the following GEO entries: GSM749688 (CTCF), GSM1010843 (PU.1) and GSM736626 (DNaseI hypersensitivity)., The basic data processing was performed similarly to H3 ChIp-seq, with a difference that these were single-end reads, and the sequencing was to a smaller depth (30–40 mil […]

Pipeline specifications

Software tools Bowtie, NucTools, HOMER
Organisms Homo sapiens
Chemicals Hydrocarbons, Acyclic, Terpenes, Carotenoids, Hydrocarbons, Cyclic