RNA-seq Data Replicates

Hello! Does DepMap Portal have biological replicates for RNA-seq gene expression datasets? I am curious because it seems that after Q3 2019 the raw counts are quite different for each cell line compared to Q2 2019 and earlier. Did that paper report entirely new RNA-seq data on top of what was already in DepMap Portal, or was it simply the same data run through a different analysis pipeline?

Thanks in advance for your clarification.

Hello akristof3,

DepMap doesn’t have biological replicates, 2019 was quite some time ago but I believe the change was due to a pipeline switch. We reprocessed everything through the same pipeline to reduce batch effect.

Hope it helps,