DepMap Portal Datasets

Resources Getting Started
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The DepMap project continuously generates new data and tools as well as integrates existing data into the DepMap framework.

All datasets either generated or integrated by DepMap are available to use in the DepMap portal. However, not all data in the DepMap portal is continuously updated. Datasets with * below are expected to continue to grow with each release.

Additionally, many data that are available to use in Data Explorer 2 and other portal tools are aggregate datasets. On the Downloads page you may select each dataset individually. If you would like to select combined datasets, please use Custom Downloads.

Below is a description of each individual dataset in the DepMap portal:

DepMap Releases (CRISPR + Omics)

  • DepMap Public* - The public DepMap Release dataset. This dataset defaults to the current version, but previous versions are available. We always recommend using the most current version of the DepMap release datasets for the most up-to-date information.

RNAi Screens

  • DEMETER2 Data v6 - Genetic dependencies estimated using the DEMETER2 model. DEMETER2 was applied to three large-scale RNAi screening datasets: the Broad Institute Project Achilles, Novartis Project DRIVE, and the Marcotte et al. breast cell line dataset. This dataset contains all data from Achilles 2.20.3, Achilles 2.4.3 and 2.0.
  • Achilles 2.20.2 - This dataset supports a publication. You can access the publication here.
  • Achilles 2.4.3 - Contains 216 lines using quantile normalization, 54k shRNA library, next-generation sequencing deconvolution.
  • Achilles 2.0 - Contains data from Phase 2 of the Achilles pooled RNAi study.

Drug Screens

  • PRISM Repurposing Primary Screen - The initial phase of PRISM Repurposing Screen, consists of the viability values for 6,790 compounds at various stages of development. All compounds are screened at 2.5 uM dose across 446-898 cell lines. Please see Corsello et al. for details.
  • PRISM Repurposing Secondary Screen - The secondary phase of PRISM Repurposing screen, covering 1,482 of the initial compounds screened against 448-724 cell lines. For each of the compounds, a PRISM viability read-out is measured at 5-day for 8 dose points with 4-fold fixed dilution starting from the top dose of 10 uM. Please see Corsello et al. for details.
  • Pharmacological Profiling - Pharmacologic profiles for 24 anticancer drugs across 504 cell lines as part of the CCLE project. You can access the publication here.
  • Sanger GDSC1 and GDSC2 - The Genomics of Drug Sensitivity in Cancer Project (GDSC) represents results from large scale viability screens across hundreds of cell lines.This dataset (Release 8.1, Oct 2019) was reprocessed to obtain dose-response parameters. Data was obtained from the Genomics of Drug Sensitivity in Cancer Project website.
  • CTRP CTD^2 - Cancer Therapeutics Response Portal (CTRP) data were obtained from the National Cancer Institute’s CTD^2 Network Open-Access Data Portal (Version 2.0, December 15th 2015 version) and represent viability data for 907 cell lines and 545 chemical perturbations.
  • Sanger Drug Combinations 2022 - Sanger drug combination data from Jaaks et al. 2022.

Other Omics

  • TelSeq Telomere Content - Telomere content estimates from running Telseq on CCLE WGS and GDSC WES data. Raw and log2-transformed telomere content estimates are provided. For more information, see Hu et al., (eLife, 2021).
  • CCLE arm-level CNAs - Expanded characterizations of CCLE cancer cell lines. Arm-level CNAs for which each chromosome arm is called as having copy gain (+1), loss (-1), or no change/no call (0) relative to background ploidy. Calls are derived from ABSOLUTE copy number profiles published in Ghandi et al., (Nature, 2019).
  • CCLE 2019 - Expanded characterizations of CCLE cancer cell lines. Includes RNA sequencing, whole-exome sequencing, whole-genome sequencing, reverse-phase protein array, reduced representation bisulfite sequencing, microRNA expression profiling, global histone modification profiling, and metabolomics. Raw sequencing data is available through the Sequence Read Archive: PRJNA523380.
  • Fusion - This is an original CCLE dataset. Contains fusions calls generated using the STAR-Fusion pipeline. Both filtered and unfiltered datasets are available.
  • Methylation (RRBS) - This is an original CCLE dataset. Reduced representation bisulfite sequencing data measuring gene methylation profiles.
  • Protein Array (RPPA) - This is an original CCLE dataset. Reverse Phase Protein Array (RPPA) data.
  • miRNA expression - This is an original CCLE dataset.
  • DNA Copy Number - This is an original CCLE dataset. Inferred copy numbers from Affymetrix CEL files converted to a single value for each probe set representing a SNP allele or a copy number probe.
  • Cell Line Annotations - This is an original CCLE dataset. Contains cell line metadata.
  • Binary Calls for Copy Number and Mutation Data - This is an original CCLE dataset.
  • Hybrid capture sequencing - This is an original CCLE dataset.
  • Oncomap mutations - This is an original CCLE dataset.
  • mRNA expression - This is an original CCLE dataset.

Other CRISPR Screens

  • Sanger CRISPR (Project Score) - Sanger KY library CRISPRCas9 KO screens from Sanger’s Project Score portal processed using Sanger QC.
  • Achilles 3.3.8 - This dataset supports a publication. CRISPR-Cas9 screens with theGeCKOv2 sgRNA library in 33 cancer cell lines.
  • Achilles Avana Screens - Genome-wide CRISPR-Cas9 screens with the Avana sgRNA library in 341 cancer cell lines.
  • Achilles GeCKO Screens - CRISPR-Cas9 screens with theGeCKO library in 43 cancer cell lines.

Other

  • Proteomics - Quantitative profiling of thousands of proteins by mass spectrometry across 375 cell lines from Nusinow et al., 2020.
  • MetMap - Dataset describing organ-specific metastasis patterns of human cancer cell lines in immunodeficient murine models.
  • Microsatellite Instability - MSI status of cell lines using next-generation sequencing (CCLE) and PCR-based phenotyping (GDSC) from Chan et al., 2019.
  • Harmonized Public Proteomics [vers.] - This file set contains all proteomic datasets DepMap has gathered over the years, with unified indexing by UniProt IDs for better integration in Data Explorer.