Study

RNA sequencing and Illumina 2.5M SNP array data collected from 675 commonly used human cancer cell lines.

Study ID Alternative Stable ID Type
EGAS00001000610 Other

Study Description

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels2–4, the transcriptome – which represents the active program of a cell – remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical ... (Show More)

Study Datasets 3 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001000725
This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000
Illumina HiSeq 2000 675
EGAD00001001013
RNAseq and exome sequencing data of gastric cancer cell lines.
Illumina HiSeq 2000 30
EGAD00010000951
SNP array data for 668 cancer cell lines
Illumina 2.5M 668

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Publications

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