DepMap Expression Public 20Q2

Q&A
1

Hello,

I was wondering what the data from Expression public 20Q2 is based on. How do they measure expression levels of each gene, is it based on RNA, protein levels, or something else? Is there anywhere I could find the methods for obtaining this dataset?

Thanks!!

2

The data is based on RNA. We take the bam file, align it to hg38 using STAR, and apply RSEM to get TPM values. The values reported in the expression files are log2(TPM+1).

You can take a look at our pipelines here.