What are those ERCC genes in RNASeq data of 21Q1?

Q&A
1

Hi, there:

for some reasons, I have to analyze the old RNAseq data from 21Q1 and I used DESeq2 package. In one of contrasts, there are lots of ERCC alike genes showed up in my differential gene list. They look like below:
ERCC.00171
ERCC.00113
ERCC.00046
ERCC.00071
ERCC.00004
ERCC.00078
…

Based on URL: Announcing the 22Q4 Release!, it was mentioned: DepMap has rebuilt the STAR and RSEM indices with reference genome that includes ERCC spike-in annotations and excludes ALT, HLA, and decoy contigs…
I realized that those are likely ERCC spike-in, since their annotations not like other genes in format as LAPTM4A…ENSG00000068697., GPD1…ENSG00000167588…

I just want to double check with you guys to make sure,

Thx and best
Ming

2

Hi Ming,

Sorry for the late reply - you are correct.

Thanks,
Simone