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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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integerate scRNA seq with FACS #7404

Closed omaaribra closed 1 year ago

omaaribra commented 1 year ago

Hi— In Hao et al, Nat Biotech 2023, you discussed the possibility of integrating scRNA-seq with other single-cell proteomics such as CODEX or CITE-seq. Given the wide use of FACS, I am asking about the feasibility of integrating scRNA-seq and flow cytometry data. Is that possible and how? Is there a recommended analysis step that can help with such an analysis? Thanks!

tomashhurst commented 1 year ago

Hey @omaaribra , very cool question. Quick clarification: are you interested in integrating ADT data (i.e. protein expression) from say CITE-seq data, with FACS data? Or are you looking to integrate RNA expression data with FACS? For the former, yes this is definitely doable, we can give some guidance for doing this in Seurat. The later is a bit more complicated, we have some solutions but it's not straight forward.

omaaribra commented 1 year ago

Hi @tomashhurst, I am actually interested in the latter. Is it possible?

yuhanH commented 1 year ago

hi @tomashhurst Here is the related issue that we discussed about Cytof-RNA integration. https://github.com/satijalab/seurat/issues/5697

kashishdoshi commented 1 year ago

Hey @tomashhurst I was wondering how would you do the former? I would like to integrate CITE-seq ADT data with CyTOF data. I assume that the CyTOF and FACS data should have a similar workflow!