About 'Estimated Number of cells' in snRNA-seq
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2.3 years ago

Hi all,

I am analyzing single nucleus RNA-seq data using Seurat. And I have total four group and 24 samples (Brain region A Control & case and Brain region B Control & case; each n=6).

I wonder what is the appropriate range of the 'Estimated number of cells' for analysis. In our analysis, Each group has slightly different average number of cells. (A Con: 17,000, A case: 9,900, B Con: 10,000, B case: 9,500) And minimum 5,700 ~ maximum 24,000 in all samples.

So, 1) What is the appropriate range of the number of cells? 2) Is it okay if there is a difference in the number of cells between groups? and 3) What should be done if the number of cells is too high or if the difference in cell number between groups need to be reduced?

Thank you in advance!

snRNA-seq scRNA-seq QC • 728 views
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I'm assuming this is 10X? The estimated number of cells would be roughly the number of cells loaded onto the chip. From there cell recovery can be anywhere from 30-80% in my experience depending on sample quality.

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Yes it is 10X and 'Estimated number of cells' is the value in 'web_summary' file produced by CellRanger. Is 'Estimated number of cells' the number of cells loaded onto the chip?? As far as I know, 'Estimated number of cells' is the number of cells before filtering used in analysis. Please let me know if I misunderstood your answer because I am newbie.

Thank you.


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