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gCSI

Acronym

The Genentech Cell Line Screening Initiative (gCSI)

Description

The Genentech Cell Line Screening Initiative (gCSI) was undertaken independently of CCLE and GDSC to to address the concerns of inconsistencies across large-scale pharmacogenomic studies. In gCSI, Genentech independently characterized the response of 410 cancer cell lines to a subset ‚Äčagents tested by GDSC and CCLE. Genentech also evaluated three specific aspects of the screening protocols that are relevant to measured drug response: readout of cell viability (metabolic versus DNA content), seeding density strategy, and cell culture media conditions.

Resource

compareDrugScreens package

RNA-seq data

RNA-seq and SNapp array data

Publication

A comprehensive transcriptional portrait of human cancer cell lines, Nature Biotechnology 2015

Reproducible pharmacogenomic profiling of cancer cell line panels, Nature 2016

Data types

Data Type Assay/Platform Raw Processed
Pharmacological CellTiter Glo Yes AUC, IC50
mRNA Expression Illumina RNA-seq Yes VSN/DESeq counts, RPKM
DNA Copy Number Illumina 2.5M SNP Yes PICNIC
DNA Mutation Sanger No CSV

PharmacoGx

PharmacoSet object for: gCSI