Question: Single Cell mRNA Seq basic question
0
gravatar for CuriousSeq
5 months ago by
CuriousSeq0
CuriousSeq0 wrote:

If an average human somatic cell has approximately 12k transcripts of mRNA floating around, how do we (for example) get a mean reads per cell of 100k? Shouldn't you get 12k mean reads per cell

rna-seq • 291 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by CuriousSeq0
3

Number of reads you will get is very different than the number of transcripts due to shearing the DNA and PCR amplification.

ADD REPLYlink written 5 months ago by goodez390

So are two reads with the same UMI considered two reads or one read?

ADD REPLYlink modified 5 months ago • written 5 months ago by CuriousSeq0
1

They are two reads but they originated from the same fragment.

ADD REPLYlink written 5 months ago by genomax58k

there are lots of other non-mRNA transcript floating around in the cell (and yes despite poly-A capture you will pick some of them up as well)

EDIT: ok, my bad, indeed number of reads is something very different than number of transcripts as goodez said.

ADD REPLYlink modified 5 months ago • written 5 months ago by lieven.sterck3.1k

I have seen estimates of 500k transcripts. It will vary by cell type, though. And, as others have pointed out, one transcript can produce multiple reads.

ADD REPLYlink written 5 months ago by igor7.0k
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