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Question: Transformed cancer cell-lines RNA-seq database
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gravatar for ever_wudi
12 months ago by
ever_wudi • 10
ever_wudi • 10 wrote:

Hi,

I am trying to find a database which has RNA-seq data for cancer cell-lines transformed from normal cells by specific oncogenes or mutated tumor suppressors. I'm not looking for RNA-seq on patient cells (like in TCGA) because they contain many other mutations so the cancer formation is hard to be attributed to a particular gene mutation. Does any body know a potentially good RNA-seq/microarray database for man-made transformed cancer cell-lines?

Thanks! Di
rna-seq genome • 520 views
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modified 12 months ago by jared.andrews07 • 2.8k • written 12 months ago by ever_wudi • 10
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gravatar for jared.andrews07
12 months ago by
jared.andrews07 • 2.8k
St. Louis, MO
jared.andrews07 • 2.8k wrote:

I don't know of a database specifically for transformed cell lines - you might be better served by identifying such cell lines and looking for expression data for them. Genentech published RNA-seq for over 600 cell lines here, so it's likely at least a few of those might be what you need.
ADD COMMENT • link written 12 months ago by jared.andrews07 • 2.8k

This is somewhat tangential, but do you know if they have the FASTQs available? It seems like they should, but I couldn't find them. I saw links to the raw counts, but not the raw reads.

ADD REPLY • link written 12 months ago by igor ♦ 8.1k
1

A lot of raw sequence data is still controlled access, so you have to jump through some hoops to get it. All the experiments in Expression Atlas have their raw sequencing data in EGA (the European Genome-phenome Archive), and you can usually find the dataset by searching for the Expression Atlas experiment. So for the Genentech cell lines above (experiment E-MTAB-2706), their sequencing data can be found here. These pages will have info for who you need to contact to get access if they're controlled access.

ADD REPLY • link written 12 months ago by jared.andrews07 • 2.8k

Thank you. That was very helpful.

ADD REPLY • link written 12 months ago by igor ♦ 8.1k

This can be a very useful site and your suggested way makes sense. Thanks a lot, jared.andrews07 (thumb up)!

ADD REPLY • link written 12 months ago by ever_wudi • 10
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