Re-analysis of multiple scRNAseq data

Question

[SG]

Hi all,

Is it possible to recombine several old scRNA seq studies and answer a biological question i.e. build up a new analysis on the basis of combine analysis of old.

EXAMPLE -I found many single cell RNA seq studies which focus on different tissues.

Can I combine them all to check gene expression of geneX in the different tissues showing relative expression in them.Is it a possible insilico study?

Will there not be a lot of batch effect?If so how can it be avoided?

Will I have to start from gene count or download SRR so that all different scrnaseq studies are quality controlled in the same manner?

Kindly guide.

Answer 1

[Igor]

Will there not be a lot of batch effect?

Most likely, yes. Depends on the protocols, differences between the labs, etc.

If so how can it be avoided?

Can't be avoided, but you could try regressing it out or bringing the data into the same "integrated" space. Check out BBKNN, Scanorama, Harmony, Seurat, Combat, MNN. I think it's hard to say which tool will work best for you, that depends on the tissue, number of samples, and other factors.

Will I have to start from gene count or download SRR so that all different scrnaseq studies are quality controlled in the same manner?

I'm not an expert, but I'm willing to speculate that CellRanger processing is uniform throughout different studies. So you could start from the count matrices if you're dealing with 10x data.

[SG]

Thank you so much for the detailed reply and great suggestions.Very helpful !