Dog Brain ChromHMM chromatin states files

<p dir="ltr">This dataset contains:</p><ul><li>Optimal peak files for H3K27me3, H3K4me3, H3K27ac histone marks from ChIP-Seq, as well as peaks from ATAC-seq data, output from MACS2 peak caller, for 8 distinct regions of the dog brain: Anterior cingulate gyrus (ACG), cerebellum, frontal lob, hypothalamus, occipital cortex, striatum, temporal cortex, and thalamus.</li><li>ChromHMM bed file outputs defining chromatin states for each of the 8 brain regions.</li></ul><p dir="ltr">The most informative ChromHMM model identified nine distinct chromatin states, numbered 1-9 in the bed files:</p><p dir="ltr">States 1, 4, 6: Promoters</p><p dir="ltr">States 2,8: Enhancers</p><p dir="ltr">State 3: Open chromatin (only ATAC signal)</p><p dir="ltr">State 7: No signal</p><p dir="ltr">State 9: Repressed</p><p dir="ltr">Data is on CanFam4 (UU_Cfam_GSD_1.0) coordinates</p><p>################################################</p><p dir="ltr">We also include here bed files containing chromatin states for 11 tissues called on the CanFam4 reference genome using raw data from the EPICdog project: github.com/snu-cdrc/dog-reference-epigenome</p><p dir="ltr">Files are named: [tissue]_13_dense.bed</p><p dir="ltr">They originally called their states on CF3, so we remapped their data to CF4, called peaks using the same ENCODE pipeline, and ran the peak files through ChromHMM, selecting a model with 13 states.

The states represent the following signals:</p><p dir="ltr">statetype</p><p dir="ltr">1Bivalent TSS/Enh</p><p dir="ltr">2Repressed polycomb</p><p dir="ltr">3Repressed</p><p dir="ltr">4Heterochromatin</p><p dir="ltr">5ZNF genes + repeats</p><p dir="ltr">6Weak TSS</p><p dir="ltr">7Flanking active TSS1</p><p dir="ltr">8Flanking active TSS2</p><p dir="ltr">9Active TSS</p><p dir="ltr">10Quiescent</p><p dir="ltr">11Active, weak enhancer</p><p dir="ltr">12Active, strong enhancer</p><p dir="ltr">13Active, poised enhancer</p><p dir="ltr"><br></p>