Can Clones be considered as replicate in RNA Seq analysis

Question

[jaganlakshman]

Hi everyone,

I have derived six single cell clones based on their ability to grow in soft agar and performed RNA seq for each clones. Can these clones be considered as biological replicates in DESeq 2 to determine the differential gene expression as compared with control library (as replicate).And these clones clustered together in PCA.

Does usually people do this or each clone should be considered as separate entities. I donot have technical replicates for each clones. If anyone could also give me a link to publications which does this way. I am not exactly sure how to search this query in pubmed.

Lakshman

Answer 1

[Irsan]

From a statistical point of view yes this is possible and also in DEseq. But I think this question should be approached as a biological question, not statistical. Biologists among each other Often disagree what are biological and technical replicates. Anyway, I think if you have 6 clones from a petri dish you can only generalize your results over other (not sampled) clones of that petri dish. You cannot extrapolate your results to other petri dishes. I guess that 1 petri dish is 1 experiment, Maybe its better to sample 6 clones from seperate petri dishes.