Does input rna concentration change expressions analysis?

Question

[badribio]

Is there a relation between the quantity of rna/cdna that is used for library prep to number of reads that you seqeunce/quantify? for example: sample a and b are biological replicates 10ng cdna was used for sample a and 20ng for sample b will you see an increase in number of reads mapping to a given gene?

Answer 1

[swbarnes2]

Assuming the quality is about the same, if you put in more than the minimum for that library protocol, it won't much matter much how much you put in. What matters more is how much library gets loaded on a flow cell, and what % of the lane/run it takes up.

[badribio]

That makes sense, we ran in to a different problem when we plot the TPM's for each transcript between two different concentration (same biological replicate) there are some genes that have higher TPM in the sample with more input RNA.