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bioinfo-biols / SEVtras

sEV-containing droplet identification in scRNA-seq data (SEVtras)
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Does SEVtras apply to data generated by STRT-seq or SMART-seq2? #24

Open SayaGoodBye opened 1 month ago

SayaGoodBye commented 1 month ago

Hello, Dr. He. Sorry to bother you again. I already knew that SEVtras would work with single cell RNA sequencing data produced by the 10x genomics chromium , which is based on droplet sequencing, but I didn't know if SEVtras would work with SMART-seq2 or STRT-seq. From what I have learned so far, STRT-seq uses single tubes and 96 cells captured via C1 microfluidic chip for single-cell RNA sequencing. In this process, could sEV not be sequenced separately as it is in the droplets produced in the 10x genomics chromium process? I really want to know that.

RuiqiaoHe commented 1 month ago

In my opinion, SEVtras can be extended to microwell-based scRNA-seq. The key to determining the application scenario for SEVtras is whether sEVs have been filtered out in the experimental procedure. The cell-free droplet or microwell would have a chance of capturing sEVs. In your description, STRT-seq with C1 microfluidic chip may be OK for SEVtras, although I haven't tried it myself.