Computational protocol: SMARCAD1 is an ATP-dependent stimulator of nucleosomal H2A acetylation via CBP, resulting in transcriptional regulation

Similar protocols

Protocol publication

[…] Sequenced reads were mapped to the Drosophila genome (UCSC genome browser assembly dm 6, BDGP Release 6) using the Burrows-Wheeler Alignment v0.7.5 (BWA) program, with default “aln” and “samse” parameters. We used the Model-based Alignment of ChIP-Seq (MACS) program to call peaks for SMARCAD1 and CBP. The following parameters were used: macs; t, treatment_bamfile; c, control_bamfile; bdg; P = 0.05.After identification of SMARCAD1 and CBP peak regions, annotation of these peaks was performed using the R package ChIPpeakAnno. This software partitioned the genome into six discrete regions based on annotated UCSC coordinates: (1) Downstream, downstream of the TES; (2) IncludeFeature, contains gene-coding sequence; (3) Inside, intergenic; (4) OverlapEnd, overlapping with the TES; (5) OverlapStart, overlapping with the TSS; (6) Upstream, upstream of the TSS. The software then output the localization attributes of the nearest features according to the partitions. […]

Pipeline specifications

Software tools BWA, ChIPpeakAnno
Databases BDGP UCSC Genome Browser
Application ChIP-seq analysis
Organisms Drosophila melanogaster
Chemicals Adenosine Triphosphate