GSM8085815: MM029 Bio-Lurbi Rep 2; Homo sapiens; OTHER
Chem-Mapping and Cut&Tag experiments were performed using the Active Motif CUT&Tag-IT assay kit (53160, 53165), following the manufacturer's instructions. ATAC-Seq experiments were performed using the Active Motif ATAC-Seq Kit (53150), following the manufacturer's instructions. Libraries were sequenced on an Illumina NextSeq 2000 sequencer as paired-end 50 base reads. Image analysis and base calling were performed using RTA version 2.7.7 and BCL Convert version 3.8.4. The adapter sequence: CTGTCTCTTATA has been trimmed with cutadapt 1.18 with option: -a CTGTCTCTTATA -A CTGTCTCTTATA -m 5 -e 0.1 and Bowtie2 parameter: -N 1 -X 1000, was used for mapping to the human genome. After the mapping, reads overlapping with ENCODE blacklist V2 were filtered. Each de-duplicated read was extended to its fragment size. Tracks were normalized with RPKM method. Peak calling was performed using Macs2 2.2.7.1 in BEDPE and narrow mode. narrowPeaks from biological triplicate samples were then merged to a single master peak set. BEDtools was used to calculate the read coverage for each peak and for each sample. Peaks were annotated using Homer software with ucsc 6.4 gene annotation. Bigwig tracks were generated using bamCoverage from deepTools 3.5.4. ATAC-Seq samples were analyzed using the ENCODE ATACseq pipeline release v2.0.2 .