Follow

Has anyone been able to perform RNA sequencing (either bulk or single cell) or ATAC sequencing (bulk or single cell) on human PBMCs stored in proteomic stabilizer reagent?

Smart Tubes were not specifically developed with RNA or DNA recovery in mind, but we have had reports of good RNA integrity numbers and even some groups having some success with RNAseq and in the following article the authors found that they were able to analyze HIV RNA and DNA in sections banked with the Smart Tube Proteomic Stabilizer (PROT1) which is the same reagent that is in the ampoules of Smart Tubes:

 

Vasquez, Joshua J., et al. "Elucidating the burden of HIV in tissues using multiplexed immunofluorescence and in situ hybridization: methods for the single-cell phenotypic characterization of cells harboring HIV in situ." Journal of Histochemistry & Cytochemistry 66.6 (2018): 427-446. 

 

One pharma customer has come up with a protocol (that they keep talking about publishing, but keep putting off in spite of my prodding) that works great for recovering RNA, but only when the starting material is PBMC; they haven't been able to get it to work as well with whole blood but it isn't yet clear whether the problem is with the plasma, grans or some other component of whole blood that is removed by ficoll separation.  Similarly a group at Stanford was able to achieve good RNA integrity numbers when starting with PBMC or other purified cells, but not when working with whole blood.

 

PROT1 does have fixative activity so that may present problems for some DNA recovery and analysis approaches, but it should be more straightforward than if you were starting with FFPE sections and there are groups getting decent data from FFPE sections.

 

I'd recommend starting by taking a close look at the publication above.   

 

You can view our publications page on our website : https://www.smarttubeinc.com/publications.htm

 

0 Comments

Article is closed for comments.
Powered by Zendesk