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.