Figure 2. Perturb-ATAC screen for control of accessibility landscape by transcription factors, long non-coding RNAs, and chromatin regulators.
(a) Histogram of total guide barcode (GBC) reads per cell. (b) Histogram of the second most common GBC identified in each cell. Cells on the low end of the distribution express a single guide RNA, while cells on the high end express two guide RNAs. (c) Scatter plot of ATAC fragments and fraction of fragments in peak regions. Cells are colored by GBC read count. (d) Heatmap of cells (rows) versus GBCs (columns) indicating proportion of reads associated with each barcode. (e) Left: volcano plots showing significantly altered genomic features between cells carrying non-targeting (NT) guides and guides targeting EZH2, SPI1, and EBER2 (FDR <= 0.025). Right: scatter plots of mean accessibility versus accessibility fold change of individual genomic peaks. (f) Heatmap of perturbed factors (rows) versus genomic annotations (columns) indicating difference in accessibility between perturbed and NT control cells. Only annotations significantly altered in at least one perturbation are shown. (g) Heatmaps indicating number of significantly altered features (left, absolute log2FC >= 1.5, mean reads/cell >= 0.4), number of altered genomic regions (middle, absolute chromVAR deviation Z >= 0.75, FDR <= .05), or quantification of the ratio of flanking to central nucleosome occupancy at altered peaks (right) for each single perturbation.