We are about to initiate #scRNAseq on some T-cell types. Back to literature, I found a wide diversity in the counts of the anlaysed cells used for the method (1K - 25K cells). I would really be happy to receive experts suggestions and hints regarding this problem.
This is both a technical and practical question.
If you are using any method that is based on distributions of cells (for example 10X), then what you do during analysis is essentially that you put a certain number of beads (cells) into urns (droplets) and you like to avoid getting two cells in the same well. If you add around 5000 cells you get around 5% of these as doublets (i.e. 250). If you add less - lower proportion of doublets but less events.
The second question is the number of cells needed for meaningful analysis. Here the question is rather how many cells there is in each subgroup (i.e. how many of your cells are Th2 cells). You usually would like to have at least 50-100 "good" cells in a group to analyse to get meaningful information on expression of rare transcripts (since you will not see the transcript in all cells). This also means that if you use a method that give you more transcripts per cell, you may get away with fewer cells.
Mats Bemark
Thank you very much for answering my question. I will take the information you mentioned in great consideration.
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