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. 2020 Dec 8;11:6274. doi: 10.1038/s41467-020-20048-9

Fig. 2. SAMMY-seq preferentially isolates heterochromatic domains.

Fig. 2

a Visualization of SAMMY-seq enrichment signal along with multiple chromatin marks on a representative region (12 Mb region in chr5:158000000-170000000). From top to bottom: tracks for open chromatin (ATAC-seq and DNase-seq – orange and brown); association to the lamina (Lamin A/C and Lamin B1 ChIP-seq – dark blue and blue); ChIP-seq for histone marks associated to PcG regulation (H3K27me3 – light green), active chromatin (H3K4me1 – dark green) or heterochromatin (H3K9me3 – light blue); SAMMY-seq enrichment signal (S4 vs S2) in 3 control samples at indicated passages (p19-20) (blue or yellow colored track for enrichment or depletion, respectively, over the S2 reference baseline). Gray boxes under each SAMMY-seq track show the SAMMY-seq domains. For ChIP-seq data, the (ChIP – input) reads distribution was computed with SPP package and we are limiting the y axis range to zero as a minimum value. See the “Methods” section for details of each type of signal processing. b Genome-wide kernel correlation (StereoGene) for SAMMY-seq of all control samples at indicated passages (p19-20) (S4 vs S2 enrichment) compared to ATAC-seq, DNase-seq, and ChIP-seq (Lamin A/C, Lamin B1, H3K27me3, H3K4me1, and H3K9me3). Here we are presenting a subset of data reported in Supplementary Fig. 2a containing a more extended and detailed comparison. For Lamin A/C and Lamin B1, we are reporting the average correlation across multiple data sets (see Supplementary Fig. 2a for individual data sets). c Overlap (Jaccard Index - JI) of three biologically independent (labels on top) control samples SAMMY-seq domains (S4 vs S2) with Lamin-Associated Domains (LADs) (Lamin A/C or Lamin B1 ChIP-seq enrichment domains). For Lamin A/C and Lamin B1, we used a consensus set of regions for each (see “Methods” section). The observed JI (blue bar) is compared to mean JI across 10,000 randomizations of SAMMY-seq domains (pink bar) or LADs (yellow bar) positions along the genome to compute empirical p-values for the probability of the observed JI being larger than the random expectation. All one-tail empirical p-values were significant (p < 0.0001). The whiskers over the randomized values show the mean ± 2 SEM interval.