How to get 2 seurat objects into a DEseq

Question

[He11oJe11o]

Kind of new to R so please forgive me, but I've completed analyzing 2 seurat objects, experimental and control. I then used celldex to get some specific labels for my clusters, and I set these as the identity in the metadata of both seurat objects (they're the same cells of course). If I want to find differentially expressed genes between the same cell types between conditions how do I go about doing that? I know that I have to merge the two, but because I want to retain the celldex identities, I'm thinking of adding a new column for the condition? Any help or references I can use?

Answer 1

[ultraanfibio]

Its probably best practice to read all samples into the same seurat object, then do the clustering and asign the cell type labels. Anyways if you got 2 seurat objects and want to merge them Seurat has functions to do that: https://satijalab.org/seurat/articles/integration_introduction.html . You can add a new metadata column as you mention ("experimental"-"control"), maybe a second column pasting condition+cell_type and do the comparison all cell_type_1_control vs cell_type_1_experimental with FindMarkers function as usual. Alternatively if you want to use DEseq2 you can create pseudobulk profiles for each sample and cell type with AggregateExpression function, then do the comparison with DESeqDataSetFromMatrix. Although comparison between pseudobulks derived from very different cell numbers will probably be problematic.