ATAC-seq of Mus musculus embryonic cell types in response to Pbx1 knockout
ATAC-seq was performed, mapped, and analyzed as previously described (PMID: 34446717: \"ATAC-seq was performed on 50,000 cells per replicate as described in Buenrostro et al. (with modifications based on Corces et al.), on EpiSCs and PSM-differentiated cell populations at desired time-points. Libraries were generated using the Ad1_noMX and Ad2.1–2.16 barcoded primers64 and amplified for 10 total PCR cycles. Libraries were purified with AMPure XP beads to remove contaminating primer dimers and fragments >1,000?bp. Library quality was assessed using the Fragment analyzer and quantitated by Qubit assay. The libraries were sequenced with 50?bp paired-end reads on a Next-Seq 500 Sequencer (Illumina) at the DanStem Genomics Platform (University of Copenhagen, Copenhagen, Denmark).\"). For all conditions, two biological replicate samples were collected from independent experiments. Library quality was assessed using the Fragment Analyzer and quantitated by Qubit assay. The libraries were sequenced with 50 bp paired-end reads on a NextSeq 500 Sequencer (Illumina) at the DanStem/reNEW Genomics Platform (University of Copenhagen, Copenhagen, Denmark). Prediction of cis-regulatory elements (CREs) and gene annotation was done using rGREAT (v4.0.4) [PMID: 20436461],[PMID: 36040971] or HOMER (v.4.7)[PMID: 20513432]