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. Author manuscript; available in PMC: 2022 Sep 24.
Published in final edited form as: Nat Biotechnol. 2022 Mar 24;40(8):1220–1230. doi: 10.1038/s41587-022-01250-0

Figure 3: scChromHMM annotates chromatin states at single-cell resolution.

Figure 3:

(A) Chromatin states returned by ChromHMM, which was run on 25 pseudobulk tracks for six histone marks. States can be broadly grouped into five categories. (B) Correlation comparing cell type-specific pseudobulk profiles of H3K4me1 in CD14 monocytes, generated from the original experiment, or from the interpolated values. Each point corresponds to a 200bp genomic window (Supplementary Methods) (C) For each cell type, the interpolated and original profiles are highly correlated and clustered together. (D) scChromHMM outputs at the PAX5 locus. (Top) Pseudobulk profiles for six chromatin marks in three cell types. Yellow bar highlights a 200bp genomic window near the TSS. (Bottom) scChromHMM posterior probabilities representing the annotation for the highlighted window in each cell. The region is uniformly annotated with a promoter state in B cells where PAX5 is transcriptionally active, and as a repressive state in other cell types. (E) Metaplots exhibiting the enrichment of chromatin accessibility and histone modifications at functional regions identified by chromHMM (left) and scChromHMM (right) in CD14 monocytes.