Extended Data Fig. 2: Similar levels of transcription and ssDNA accumulation on normal chromosome 1 of COLO320 cell lines.
From: Enhancing transcription–replication conflict targets ecDNA-positive cancers
(a) Read density of genomic assays in COLO320DM and COLO320HSR in total counts per million (CPM) on chromosome 1, which is outside of ecDNA intervals. KAS-seq read density is shown as (CPM) of the KAS-seq relative to CPM of the input. The mean of two biological replicates is shown for GRO-seq, Ribo-Zero and KAS-seq; a single replicate is shown for WGS. (b) Metagene heatmap plot visualization of GRO-seq, Ribo Zero RNA-seq, log2 of input-normalized H3K36me3 ChIP-seq, and log2 of input-normalized coverage of KAS-seq within chromosome 1. All plots are anchored at the GRO-seq TSS as identified by HOMER. One representative biological replicate for each condition is visualized. (c) Stacked bar charts of read density in total counts per million (CPM) of GRO-seq and Ribo-Zero in COLO320DM and COLO320HSR across all chromosomes.
