title: GSM3504371: Control CM ATAC-seq rep2; Mus musculus; ATAC-seq
library_construction_protocol: Approximately 50,000 bead-bound PCM-1(+) CM nuclei were used as input for the assay for transposase accessible chromatin with high throughout sequencing (ATAC-seq). ATAC-seq libraries were generated as previously described (Buenrostro et al., 2013). Paired end 2x75 bp sequencing was performed with an Illumina Nextseq instrument (DNA Link Inc.). Reads were mapped to the mouse genome (mm10) by using Bowtie2 with default paired-end settings (Langmead et al., 2009). Next, all non-nuclear reads and improperly paired reads were discarded. Duplicated reads were removed with Picard-1174 MarkDuplicates. Peak calling was carried out with MACS2 (callpeak–nomodel–broad). Blacklisted regions were lifted over from mm9 to mouse genome mm10 and removed along with peaks of low sequencing quality (>q30 required). Reads were counted for each condition from the comprehensive peak file (YAP5SA OE and control replicates merged) by using bedtools (multicov module) (Quinlan, 2014). Quantile normalization of ATAC-seq data sets was performed with CQN (Hansen et al., 2012), and offsets were fed into DESeq2 to quantify differential accessibility (Love et al., 2014). Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015). Motif enrichment analysis was conducted with HOMER (Heinz et al., 2010) (findMotifsGenome.pl and annotatePeaks.pl). Gene tracks were shown by using the UCSC genome browser. ES cell ATAC-seq data was used from GSM1563569, with reads mapped to the mm10 genome using bowtie2 and analyzed with HOMER (annotatePeaks.pl) and Galaxy/deeptools2 (multiBigwigSummary, plotCorrelation) (Ramirez et al., 2016).
attributes.tag: GEO Accession
attributes.value: GSM3504371