Expression pattern for transcripts from 23Q2 vs 22Q4 data

Q&A
1

Dear All,
I wanted to analyze the expression of different isoforms of a specific gene in particular cell lines, and I discovered that the expression patterns are completely different for the 23Q2 and 22Q4 isoforms. Why might this be the case?
I would appreciate any help.
Best,
Irina.

2

Hi Irina,

There were no changes in the expression pipeline between 22Q4 and 23Q2. Do you mind sharing more details on what files you were using and what gene you were looking at in particular? If you were working with a subset of the cell lines, can you share the cell line ids as well? I’m happy to look more into this.

Thanks,
Simone

3

Dear Simone,
I was interested in isoforms of SNCA in neuroblastoma cell lines. I analysed OmicsExpressionTranscriptsTPMLogp1Profile.csv file from 23Q2 and CCLE_RNAseq_transcripts.csv from 22Q data. I uploaded my plots.

Screenshot 2023-11-30 at 15.09.45
Screenshot 2023-11-30 at 15.09.452132×838 174 KB

4

Hi Irina,

Is the left plot 22Q1 or 22Q2? Between 22Q1 and 22Q2 we had a big pipeline update including newer versions of STAR, RSEM, and GENCODE, which could’ve led to this change. There was also a minor update before 22Q4 for STAR and RSEM indices that might have contributed to this.

In case you haven’t looked at it already, are there many new cell lines included in the 23Q2 set?

Thanks,
Simone