Processed Seurat Object of scRNAseq data from wildtype and CaMKK2 KO immune infiltrate of CT2a preclinical murine glioma

This repository contains the processed Seurat objects generated from the raw data deposited at the Gene Expression Omnibus (GEO) under GSE197879.

Details about the experiment and sequencing are available under GSE197879.

Information on how the Seurat objects were created can be found in this GitHub repository https://github.com/wht10/CT2A_scRNAseq_CaMKK2KOvWT .

Notable metadata within each Seurat object:

1. Processed_CD45_Live_Fig2b.rds

Genotype - whether the cell is from a WT or CaMKK2 KO mouse

HTO_maxID - The biological replicate that the cell came from (4 biological replicates per genotype)

MouseID - A concatenation between the genotype and HTO_maxID, providing a unique identifier for each biological replicate

Cell.Type - The cell type annotations for each cell. Can be assigned to "Idents()" to change the name of the cell identities.

Geno.Ident - A concatenation between Genotype and Cell.Type. By re-assigning this to "Idents()"  "FindMarkers()" can be used to investigate differentially expressed genes within a cell-type between genotypes. 

2. Reclustered_TILs_Fig3a.rds

Genotype - whether the cell is from a WT or CaMKK2 KO mouse

HTO_maxID - The biological replicate that the cell came from (4 biological replicates per genotype)

MouseID - A concatenation between the genotype and HTO_maxID, providing a unique identifier for each biological replicate

Celltype - The cell type annotations for each cell. Can be assigned to "Idents()" to change the name of the cell identities.

Geno_Ident - A concatenation between Genotype and cell-type. By re-assigning this to "Idents()"  "FindMarkers()" can be used to investigate differentially expressed genes within a cell-type between genotypes.