Question: RNA-seq data from CCLE - where are the details?
E ai cara, check the original publication: The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
In particular, look at Supplementary Material 1 (Word doc) - it has information on each of the following:
Supplementary Methods 1. Cell line selection and annotation 2. DNA and RNA extraction 3. Genomic characterization SNP Arrays: DNA identity analysis by mass spectrometric SNP genotyping 4. Cell line identity validation by SNP genotyping 5. Gene set activity scores 6. Cell line-to-primary tumor comparison Copy-number comparison: Expression comparison: Mutation-rate comparison 7. Pharmacological characterization 8. Prediction of drug response 8.1. Sensitivity prediction using regression analysis 8.2. Sensitivity prediction using categorical analysis 9. AHR validation experiments Cell lines and cell culture conditions Lentivirally delivered short hairpin RNA Immunoblot analysis: Analysis of mRNA expression by quantitative RT-PCR (qRT-PCR) Growth curves Pharmacologic growth inhibition curves 10. Data sharing/release All raw and processed data are available at the CCLE website: www.broadinstitute.org/ccle In addition, the website offers direct links to data visualization tools such as IGV39, as well as genepattern-based40 analysis tools for expression and copy-number class comparison analyses.