ATAC-seq in precursor and differentiated ER-Hoxb8 cells

ATAC-seq in precursor and differentiated ER-Hoxb8 cells Overall design: Precursor and day 3 differentiated WT and C/EBPd KO ER-Hoxb8 cells were harvested, washed and cryopreserved in 50% FBS/ 40% growth media/ 10% DMSO using a freezing container at -80 °C overnight. Sequence analysis was performed by mapping the paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) to the genome using the BWA algorithm with default settings (“bwa mem”). Only reads that passed Illumina's purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were removed. BAM files were used to perform peak calling with MACS2, using paired-end mode with a bandwidth of 200 and q-value cutoff of 0.01. BedGraph files were converted to BigWig format for visualization with the Integrative Genomics Viewer (IGV) using bedGraphToBigWig. Differential accessibility analyses for all possible comparisons between WT and/or C/EBPd KO in day 0 and day 3 groups were carried out with GUAVA v1. Differential peaks were defined as those merged intervals within a window of 5000 bp upstream and 3000 bp downstream of the transcription start site (TSS) showing an adjusted p-value < 0.05 and log2 fold change = ±1.5.