Rna-Sequencing For Nci-60 Data

Question

[pm2013]

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

Answer 1

[miquelduranfrigola]

If I'm not wrong, this Cell paper includes RNA-seq data in the supplementary materials.

[pm2013]

Thanks for your reply..but I think I found my answer. You can get access to the data through cghub.

[Neilfws]

Feel free to answer your own question and select your answer as the best :)

[David Quigley]

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).

Answer 2

[Sebastian Boegel]

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?

[David Quigley]

You could check: http://www.broadinstitute.org/ccle/data/browseSamples

Answer 3

[elmbeech]

this answer was deleted. there was a mix up in the cell line panel of interest.