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cole-trapnell-lab / sci-plex

repository containing analysis scripts and auxiliary files
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some questions about the data #1

Closed XiaohanChen97 closed 4 years ago

XiaohanChen97 commented 4 years ago

This is really a nice work! But I got some questions about the data. First, I saw this in your code, but I can not find CDS file in GEO. image Second, I do want to know which file stores the gene expression matrix in each cell, is the CDS file？ Thank you for such a nice work!

sanjayrsrivatsan commented 4 years ago

Hi XiaohanChen97, I just checked and you're right. I'm trying to figure out why these files weren't uploaded to GEO. I'll leave this ticket open until I confirm with you that the CDS are posted.

jamestwebber commented 4 years ago

The method and results are very impressive, this should be a great resource. I have another data question, apologies if this is listed somewhere but I couldn't find it.

Is there conventional dose-response data available for these cell lines and drugs? I see the Fig 4 comparison between sciPlex and in vitro IC50 for the HDAC inhibitors, but was unclear on whether the same type of data were available for the other drugs, and whether those data is in this repo or needs to be retrieved from another source (LINCS?).

sanjayrsrivatsan commented 4 years ago

Hi @XiaohanChen97, Thanks again for pointing this out. We emailed GEO and the CDS is now online. Please look here for a zipped copy.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4150377

sanjayrsrivatsan commented 4 years ago

@jamestwebber we were able to manually curate the in vitro IC50 data for different HDAC inhibitors against different HDAC isoforms, however, we don't have other conventional dose-response data within the paper itself. What we do have is dose response data based on cell counts as presented in figure3. These are not gold standard estimates for estimating EC50, however, as they only include 4 doses.

LINCS may be a good place to find this.