Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
- 1. Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- 2. Department of Pathology and Immunology Faculty of Medicine, University of Geneva, Geneva, Switzerland
Description
Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC (https://doi.org/10.7554/eLife.94833.1), which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.
To evaluate EPIC-ATAC, we generated a bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:
- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt
- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt
- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt
- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak
- Bed files listing ATAC-Seq fragments for each sample: *.bed
We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide rds files containing the pseudobulks data used in our work for the evaluation of EPIC-ATAC. The rds files are located in the zip file "pseudobulks.zip".
The file "additional_data.zip" contains additional files used to generate the reference profiles in EPIC-ATAC and to reproduce the main analyses performed in the manuscript: https://doi.org/10.7554/eLife.94833.1. These files are required to run the code available on the following GitHub repository: GfellerLab/EPIC-ATAC_manuscript.
Files
additional_data.zip
Files
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