Can we compare bulk RNAseq samples and single cell rnaseq clusters?

Question

[learner.bioinformatics]

Hi folks,

I have 3 Bulk RNAseq samples from immune cells (Naive, Population1 and Population2), similarly I have two other immune populations from Single Cell RNAseq samples.

I am interested in comparing 3 Bulk RNAseq and 2 single cell RNA seq. Any thoughts, papers and suggestions are welcomed.

Thanks in advance.

[GouthamAtla]

What do you mean by "comparing" ?

Answer 1

[Kevin Blighe]

I don't know - perhaps define clusters in the scRNA-seq data, get the genes that are highly expressed in these clusters, and then check for the expression of these in the bulk data.

Similar to the above, you could also do a rudimentary de-convolution by defining a signature for each identified scRNA-seq cluster, and then use these in the bulk data in order to infer cell-types [in the bulk data].

Kevin

Answer 2

[ahmad mousavi]

Hello.

there are some tools for creating correlation between the scRNA and bulk RNA such as clustifyr or de-convolution methods such as granulator