Cell line in expression matrix with no info in sample_info table

Q&A
1

Dear DepMap team,

I was quickly checking the files I downloaded: CCLE_expression & the sample_info. I noticed that there is once CL in the expression file that doesn’t exist in the sample_info (ACH-001316) could you please check why?

thank you

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2

Hello,

Thanks for reaching out to us.

In this case, we were aware that the metadata for ACH-001316 is missing. When we investigated, we discovered this is due to ACH-001316 being the same line as ACH-001163 (where one was grown as an adherent line, and the other as a suspension)

This has resulted in some challenges with our internal tracking, as people may want to consider these lines to be the same in some contexts, but we expect they will behave different when screened.

The omission from the sample info was a side effect of how we internally organize the data and we’re still trying to figure out the best strategy to track these two, as they represent a tricky case that we haven’t encountered elsewhere. We’re still investigating how to best handle the data for these two lines moving forward.

Thanks,
Phil

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3

I’m going to add ACH-001316 to my copy of the metadata and call it the BARD cell line in honor of the many interns who worked hard to clean up past metadata challenges.

EDIT: do you know which one is adherent, which is suspension?

4

I was having the same problem with the missing cell line on sample_info, ACH-001163 has this comment in the file: “Adherent version of CCLFPEDS0001T”

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