What's the genome version and gene annotation file used for Depmap bulk RNA-Seq expression estimation?

Q&A
1

Dear Sir./Madam.,

Can I know what’s the genome version and gene annotation file (e.g. Gencode or Ensembl, which version) used for Depmap bulk RNA-Seq expression estimation?

Thanks,
Bo

2

Hi Bo,

We currently use Gencode v38 to create references for RSEM. To generate the gene-level matrices, we mapped the ENSG IDs to gene symbols and Entrez IDs using BioMart version nov2020.

Best,
Simone