Hi I am trying to see if there is any publically available RNA-seq data for NCI-60 cell lines. I tried to browse for datasets but can only find microarray data for these cell lines. Is there such data available and if yes when can I can download the raw data for these (if possible). Any help would be appreciated.
Thanks
3 answers
If I'm not wrong, this Cell paper includes RNA-seq data in the supplementary materials.
I don't think that's the case. From Experimental Procedures: Comparison of Proteomics and Transcriptomics: Normalized gene expression data for NCI-60 cell lines were obtained from the Gene Expression Omnibus (series accession number GSE32474; Barrett et al., 2009; Pfister et al., 2009).
The Cell Reports paper mentioned above uses Microarray gene expression data.
I am also searching for NCI60 RNA-Seq data. cghub was mentioned in an answer above. In case of mean: https://cghub.ucsc.edu/datasets/data_sets.html, there is unfortunately no NCI60 RNA-Seq dataset to download. Or is the NCI60 contained in the CCLE dataset?
You could check: http://www.broadinstitute.org/ccle/data/browseSamples
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