Extended Data Fig. 1: Benchmarking of Dam&ChIC data against state-of-the-art methods.
(a) Bioanalyzer plot showing the amount and size distribution of linearly-amplified RNA (aRNA), derived after in vitro transcription (see Methods). Dam&ChIC was performed to profile Dam-LMNB1 and H3K27me3, alongside respective control DamID-only and ChIC-only experiments. Each aRNA product was derived from a 384-well plate containing 380 cells, barcoded and pooled together prior to amplification. The samples were processed in parallel. (b) Comparison of the fraction of reads mapping on a genomic GATC motif (black) between Dam&ChIC, DamID-only and ChIC-only. (c) Violin plots showing a quantification of the first nucleotide of invalid DamID reads (that is, not mapping on genomic GATC motifs) for Dam&ChIC, DamID-only and ChIC-only. (d) Violin plot showing a quantification of the first two nucleotides of invalid DamID reads for Dam&ChIC, DamID-only and ChIC-only. (e) Distribution of the unique number of Dam-LMNB1 (left) or H3K27me3 (right) reads recovered per cell by DamID-only, ChIC-only or Dam&ChIC. (f) Comparison of unique number of reads obtained per cell between Dam&ChIC and other multifactorial chromatin profiling methods19,20,21,22. (g) Genomic distribution of in silico GATC mappability (top, black) and mappability of pA-MNase cut sites derived experimentally with ChIC against H3 (bottom, grey). (h) Heatmaps showing chromatin features profiled with Dam&ChIC, aligned over LADs (n = 815) that were previously defined in KBM7 cells29. Line plots indicate scaled averages of the heatmaps for each mapped chromatin feature. (i) Genomic tracks of in silico bulk Dam&ChIC profiles compared to corresponding ChIC-only datasets in KBM7 cells and corresponding ENCODE (ENCODE 2012) ChIP-seq or ATAC-seq datasets in K562 cells. (j) Tornado plots depicting in silico bulk Dam&ChIC data aligned on ENCODE ChIP-seq or ATAC-seq peak coordinates in K562 cells. Peaks (rows) are ordered on the peak signal of the corresponding Dam&ChIC dataset (that is, ATAC-seq peaks are ordered on Dam DamID data, H3K4me3 peaks are ordered on H3K4me3 ChIC data and so on). Source numerical data is available in source data.
