Human melanoma cells were grown to confluence in DMEM + 10% FCS, and ~ 1X108 cells were formaldehyde crosslinked and collected. ChIP was performed using the methods of (30 , 39 (link)) with antibodies against H3K27Ac (ab4729) (Abcam), H3K4Me1 (ab8895) (Abcam), and SOX10 (Santa Cruz Biotechnology, sc-17342x). Libraries were prepared using the NEBNext Multiplex Oligos for Illumina kit (NEB) and run on an Illumina Hi-Seq2000. Data analysis, including enhancer and super-enhancer calling, were performed as described in (26 (link)). Genomic track images were generated using the IGV package (40 (link)) and the UCSC Browser (41 (link)).
All human ChIP-Seq datasets were aligned to build version NCBI37/HG19 of the human genome using Bowtie (version 0.12.9) (42 ) with the following parameters: –n2, -e70, -m2, -k2, --best. We used the MACS version 1.4.1 (Model based analysis of ChIP-Seq) (43 (link)) peak finding algorithm to identify regions of ChIP-Seq enrichment over background. A p-value threshold of enrichment of 1e-9 was used for all datasets. Wiggle files for gene tracks were created using MACS with options –w –S –space=50 to count reads in 50bp bins. They were normalized to the total number (in millions) of mapped reads producing the final tracks in units of reads per million mapped reads per bp (rpm/bp).
All human ChIP-Seq datasets were aligned to build version NCBI37/HG19 of the human genome using Bowtie (version 0.12.9) (42 ) with the following parameters: –n2, -e70, -m2, -k2, --best. We used the MACS version 1.4.1 (Model based analysis of ChIP-Seq) (43 (link)) peak finding algorithm to identify regions of ChIP-Seq enrichment over background. A p-value threshold of enrichment of 1e-9 was used for all datasets. Wiggle files for gene tracks were created using MACS with options –w –S –space=50 to count reads in 50bp bins. They were normalized to the total number (in millions) of mapped reads producing the final tracks in units of reads per million mapped reads per bp (rpm/bp).
