GSM5941804: siBAP_EtOH; Homo sapiens; ATAC-seq
Primary analyze of ATAC-seq: The threshold of the number of the valid peak was selected within a false discovery rate (FDR) of 0.01. We used the default parameters from HOMER to distinguish genomic distribution, while promoter peaks were defined as those with peak center falling between 100 bp downstream and 5,000 bp upstream of transcript start sites (TSS). Exon, intron, and transcript terminate site (TTS) regions were exported from the National Center for Biological Information (NCBI), and the other regions were suggested as intergenic regions. To define meaningful BAP18 binding sites, we defined the fold enrichment of a peak was larger than 2 in IP versus input and the fold change (FC) of tag density was considered at least p<10e-5. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.