Fig. 2: Validation of epigenomic profiling of MSNs using published ChIP-Seq data.
From: Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum
A Representative genome browser views of different profiling methods and cell-types. Nucleus accumbens (NAc) bulk ChIP-seq data come from28. Signal is normalized to total mapped reads: Count Per Million (CPM). B H3K4me3 and C) H3K27me3 heatmap showing Pearson’s correlation coefficients among NAc ChIP-seq, D1 CnR, and A2a CnR. Two replicates are shown for each dataset. The correlation coefficients were calculated by dividing the genome into 1 kb bins and counting reads in each bin. D Enrichment of A2a and D1 CnR H3K4me3 or IgG signal centered on peaks called from NAc H3K4me3 ChIP-seq by MACS2. Top 20,000 peaks sorted by MACS2 score were used. Heatmap shows signal around individual peaks, and the averaged signal is shown above the heatmap. Two replicates of CnR data were merged. Signal is normalized by signal and variance across transcriptionally constant genes (quantile normalization). E Enrichment of A2a and D1 CnR H3K27me3 or IgG signal around peaks called from NAc H3K27me3 ChIP-seq by SICER. Peaks within 5 kb were merged to avoid double counting. Heatmap shows signal around individual peaks, and the averaged signal is shown above the heatmap. Two replicates of CnR data were merged. Signal is normalized by variance across transcriptionally constant genes (quantile normalization).
