Datasets

The majority of models within the Cancer Dependency Map at Sanger have undergone extensive characterisation including: sequencing, copy number, methylation, gene expression and drug screening. These large scale genomic and functional datasets can be explored using dedicated resources such as the Cell Model Passports, Project Score and GDSC. Processed downloads are available here and via the DepMap API. Links to repositories holding raw data are provided in the Cell Model Passports and within each dataset's documentation page.

Dataset Overview

Mutation

All sequencing data including WES, WGS & TGS used to generate mutation data for the cell line and organoid models.

Download Data: Mutation Data

Documentation: Mutation

Copy Number

Copy number data obtained using the Affymetrix SNP6 array processed using PICNIC and GISTIC.

Download Data: Copy Number Data

Documentation: Copy Number

Gene Expression

Gene expression generated from RNASeq data and processed by the iRAP pipeline.

Download Data: Expression Data

Documentation: Expression


Fusions

Gene fusions predicted using Sanger and CCLE RNASeq data.

Download Data: Fusion Data

Documentation: Fusions

Methylation

Methylation profiling of cell lines using the Illumina Human Methylation 450 BeadChip.

Download Data: Methlation Data (Raw)

Documentation: Methylation

CRISPR WG Drop-out

CRISPR-Cas9 drop-out screens in cell models identifying genes required for cell fitness.

Download Data: CRISPR: KO Data

Documentation: CRISPR Drop-out


Drug Sensitivity

Drug response data and genomic markers of sensitivity generated through large scale cell viability screens.

Download Data: GDSC Data

Documentation: GDSC


Gene Annotation & Model Authentication

Gene Annotation

Includes the DepMap cancer gene list and HUGO, Ensembl, Entrez and Refseq annotations.

Download Gene Lists: Gene Lists

Documentation: Gene Annotation

Model Authentication

How data associated with the cell models is authenticated and integrated.

Documentation: Model Authentication