Source data from Weiner et al 2024

This repository provides the processed data necessay to produce the figures from the Weiner, et al., Nature Communications paper entitled "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data".

The data is organized into directories based on figure numbers of the paper. For instance, the directory source_data/fig2_S3/ contains all data pertaining to main figure 2 and supplementary figure 3. Within each directory, subdirectories are organized by figure panel, meaning that the file source_data/fig2_S3/2fg_S3g/cell_metrics.tsv only pertains to data which appears in Fig 2f, Fig 2g, and Fig S3g.

Certain figure panels incorporate data from multiple samples. Sample ID subdirectories are used for these panels. For example, Fig S8a-c use data at the following paths source_data/fig5_S8/S8abc/{sample_id}/s_phase_bafs.csv.gz

All source code for upstream data preprocessing and downstream plotting can be found at the corresponding github repository for this manuscript: https://github.com/shahcompbio/scdna_replication_paper.In addition to source data, we are also including two additional files which contain series of sample-specific heatmaps. Below are the descriptions of each file.

Additional File 1: HMMcopy and SIGNALS heatmaps of high-quality G1/2-phase cells across all samples. Matrices of somatic copy number state called by HMMcopy (Ha, et al, 2012) (left) and allelic imbalance state called by SIGNALS (Funnell, et al, 2022) (right) for all cells in a sample. Only high-quality G1/2-phase cells are included in this analysis. The rows are sorted the same in both heatmaps to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of both heatmaps. Each page represents a unique sample in the metacohort of breast and ovarian cell lines and PDXs (Fig 4a). The sample ID and number of high quality G1/2-phase cells (i.e. SIGNALS cells) are shown at the top of each page. 

Additional File 2: PERT input and output matrices for gastric cancer cell lines at 500kb and 20kb resolution. Matrices of PERT input (left: reads per million and HMMcopy states) and PERT output (right: PERT somatic copy number and replication states) for the three gastric cancer cell lines sequenced with 10X Chromium single-cell DNA (Andor, et al, 2020). The top heatmaps on each page contains the cells predicted to be in S-phase by PERT and the bottom heatmaps contains the cells predicted to be in G1/2-phase by PERT. The rows are sorted the same in all four columns going from right to left to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of all four heatmaps. The first three pages represent PERT runs on each cell line at 500kb resolution. The final two pages represent PERT runs for two of the three cell lines at 20kb resolution. We did not run PERT at 20kb resolution for the SNU-668 cell line as there were too few S-phase cells to infer the RT profile at 20kb higher resolution.For further information please reach out to Adam Weiner ([e-mail])