5' Seq for non-immune cells

Posted By: cwkime, on Apr 18, 2019 at 1:55 AM


I am interested in getting good scRNA seq data and the 5' information would be useful for our study.   However, when I look for the 5' kit it is always discussed in conjuction with the VDJ/Immune profiling system. I am not working with immune cells.   Are there resources out there for using 5' sequencing in 10x for other cells?  


Please advise.


2 Replies

Re: 5' Seq for non-immune cells

Posted By: SShelton, on Apr 22, 2019 at 8:52 AM
Hi C,
Thanks for posting on our community board!
Both the 5' and the 3' gene expression libraries can be used for profiling many different cell types, not just immune cells. When we compared our 5' and 3' gene expression data for PBMCs, we were able to identify the same major subpopulations in the same approximate proportion in both datasets, indicating that both assays can be used to accurately assess cell populations. 
While most of our customers interested in gene expression only choose 3' as their assay of choice, if you are interested in studying TSS sites or other genetic elements at the 5' end, then 5' gene expression may be a good choice for your project.
If you're interested in looking into this further, I recommend checking out these datasets to see how they compare:
3' PBMCs
5' PBMCs

Re: 5' Seq for non-immune cells

Posted By: ERStanley, on Aug 1, 2019 at 11:55 AM

I have used 5' reagents for clients that were using Rabbit models and apparently, the Rabbit genome is more extensively annotated from the 5' direction. They were adipocytes and they worked fine.