Cancer Cell Line Encyclopedia (CCLE)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/ccle-dataset")

fs.listdir("s3://gdc-ccle-2-open")

Description:

The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. The CCLE provides public access to genomic data, visualization and analysis for over 1100 cancer cell lines. This dataset contains RNA-Seq Aligned Reads, WXS Aligned Reads, and WGS Aligned Reads data.

Contact:

The Cancer Cell Line Encyclopedia (CCLE) project is an effort to conduct a detailed genetic characterization of a large panel of human cancer cell lines. The CCLE provides public access to genomic data, visualization and analysis for over 1100 cancer cell lines. This dataset contains RNA-Seq Aligned Reads, WXS Aligned Reads, and WGS Aligned Reads data.

Update Frequency:

Genomic Data Commons (GDC) is source of truth for this dataset; GDC offers monthly data releases, although this dataset may not be updated at every release.

Managed By:

https://ctds.uchicago.edu/

Resources:

1. resource:
   • Description: RNA-Seq Aligned Reads, WXS Aligned Reads, WGS Aligned Reads
   • ARN: arn:aws:s3:::gdc-ccle-2-open
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, cancer, genetic, genomic, life sciences, transcriptomics, whole genome sequencing, Homo sapiens, STRIDES

Tools & Applications:

1. tools & applications:

   • Title: Genomic Data Commons
   • URL: https://portal.gdc.cancer.gov/legacy-archive/
   • AuthorName: National Cancer Institute
   • AuthorURL: https://gdc.cancer.gov/

2. tools & applications:

   • Title: Broad Institute Cancer Cell Line Encyclopedia
   • URL: https://portals.broadinstitute.org/ccle
   • AuthorName: The Broad Institute of MIT & Harvard
   • AuthorURL: https://www.broadinstitute.org/

3. tools & applications:

   • Title: Cancer Genomics Cloud
   • URL: https://cgc-accounts.sbgenomics.com/
   • AuthorName: Seven Bridges
   • AuthorURL: https://docs.sevenbridges.com/docs/ccle-data

4. tools & applications:

   • Title: ISB CGC BigQuery tables
   • URL: https://console.cloud.google.com/bigquery?p=isb-cgc&d=CCLE_bioclin_v0&page=dataset
   • AuthorName: Institute for Systems Biology
   • AuthorURL: https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/data/CCLE_top.html

Publication:

1. publication:

   • Title: Next-generation characterization of the Cancer Cell Line Encyclopedia
   • URL: https://doi.org/10.1038/s41586-019-1186-3
   • AuthorName: Ghandi, M., Huang F. et al.

2. publication:

   • Title: The landscape of cancer cell line metabolism
   • URL: https://doi.org/10.1038/s41591-019-0404-8
   • AuthorName: Li, H. et al.

3. publication:

   • Title: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

   • URL: https://doi.org/10.1038/nature11003

   • AuthorName: Barretina Caponigro Stransky et al.

4. publication:

   • Title: Pharmacogenomic agreement between two cancer cell line data sets
   • URL: https://doi.org/10.1038/nature15736
   • AuthorName: The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium