Content:
Overview
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
Genomic Datasets
| Dataset Type | Description | Documentation |
|---|---|---|
| Mutation | All sequencing data including WES, WGS & TGS used to generate mutation data for the cell line and organoid models. | Mutation |
| Copy Number | Copy number data obtained using the Affymetrix SNP6 array processed using PICNIC and GISTIC. | Copy Number |
| Gene Expression | Gene expression generated from RNASeq data and processed by the iRAP pipeline. | Gene Expression |
| Fusions | Gene fusions predicted using Sanger and CCLE RNASeq data. | Fusions |
| Proteomics | Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). | Proteomics |
| Methylation | Methylation profiling of cell lines using the Illumina Human Methylation 450 BeadChip. | Methlyation |
Functional Datasets
| Dataset Type | Description | Documentation |
|---|---|---|
| CRISPR WG Drop-out | CRISPR-Cas9 drop-out screens in cell models identifying genes required for cell fitness. | CRISPR Drop-out |
| Drug Sensitivity | Drug response data and genomic markers of sensitivity generated through large scale cell viability screens. | Drug Sensitivity |
| Growth rate | Cell model growth rates derived from the GDSC drug sensitivity screens. | Growth Rate |
Gene Lists & Driver Annotations
| Gene & Driver Lists | Description | Documentation |
|---|---|---|
| Full Gene List | Includes the DepMap cancer gene list and HUGO, Ensembl, Entrez and Refseq annotations. | Gene List |
| Driver Gene List | Cancer gene list used in Cell Model Passports with tumour suppressor / oncogene annotation. | Driver Gene List |
Content
Overview