K562 and human brain transcriptomes, and various epigenomes from K562 and human/mouse brain curated from public databases and re-analyzed for comparison with the single-stranded DNA open-chromatin detected by CHEX-seq

To study the association of CHEX-seq with transcriptional activity, we downloaded and re-analyzed K562 bulk RNA-seq, single-cell RNA-seq, and GRO-seq data, as well as human brain single-cell RNA-seq data. To study the association of CHEX-seq with DNA replication, we downloaded and re-analyzed K562 replication origin data. To study the association of CHEX-seq with epigenomes, we downloaded and re-analyzed ATAC-seq, DNase-seq, FAIRE-seq, RRBS-seq, DRIP-seq, ChIP-seq and super-enhancer data from K562, human and/or mouse brain. To study the association of CHEX-seq with DNA strand conformation, we downloaded and re-analyzed human and mouse non-B-form DNA regions. We downloaded human and mouse transcriptomes, epigenomes and DNA strand conformation data from GEO, ENCODE, UCSC Genome Browser and non-B DB. They are: K562 bulk RNA-seq, RNA-seq and single-cell RNA-seq samples; 88 human astrocyte and 100 human neuron single-cell RNA-seq samples; K562 ATAC-seq, DNase-seq, FAIRE-seq, RRBS-seq, DRIP-seq, replication origins and super-enhancer samples; 258 K562 TF binding ChIP-seq samples; 11 K562 narrow or broad histone modification samples; one human brain ATAC-seq sample; 5 human brain DNase-seq samples; one human brain FAIRE-seq sample; 2 mouse brain ATAC-seq samples; 3 mouse brain DNase-seq samples; 10 mouse brain narrow or broad histone modification samples; 7 human non-B-form DNA region samples; 7 mouse non-B-form DNA region samples.