CD45R isoforms in RNA-seq

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3.5 years ago

dioscorea.bulbifera ▴ 10

Hello!

I am classifying cells using human scRNA-seq data processed through cellranger, and I realize that my cleaned data only has expression information to the level of CD45R/PTPRC and does not have information on CD45R isoforms CD45RA and CD45RO which are useful for differentiating immune cell types. I do not believe that these isoforms are differentiated in the reference genome I used since they don't have different gene symbols.

Does anyone have experience with differentiating the two in RNA-seq? Would this require creating a custom reference genome?

Thanks!

RNAseq • 1.1k views

ADD COMMENT • link 3.5 years ago by dioscorea.bulbifera ▴ 10

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See this paper where those isoforms were resolved:

https://www.nature.com/articles/s41592-018-0303-9

A reference transcriptome might be more useful for your purposes (i.e. isoform-level analysis).

ADD REPLY • link 3.5 years ago by dsull ★ 6.9k

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I may be misinterpreting the comment, but where would I find a reference transcriptome that includes gene isoforms?

ADD REPLY • link 3.5 years ago by dioscorea.bulbifera ▴ 10

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