GSE158175
ScRNA-Seq of Fresh Mouse Glioblastoma Cells and Mouse Glioblastoma Cell line
Methods: In our study, we added tdTomato gene inherent in our mouse model gene list to obtain the final matrics by modifying the reference genome. Finally, we separated the matrix by the cell type judgment result obtained by the cellranger. Cells with high quality were selected with the following criteria: (1) Genes detected in < 3 cells were removed; (2) Cells with unique molecular identified (UMI) = 150 or = 4500 were removed. (3) Cells with = 20% mitochondrial counts were removed. Results:  scRNA-seq for the cells dissociated from a CKO_NG2-CreER tumor (Figure 1B) identified 12 distinct clusters, visualized using t-distributed stochastic neighbor embedding (t-SNE). Referring to known cellular markers in the brain 24, we could identify the cell identities/states of 10 clusters, including two for OPCs (C5 and C7), two for microglia (C1 and C4), one each for astrocytes (C2), endothelial cells (C3), oligodendrocytes (C6), pericytes (C9), neurons (C11) and T/dendritic cells (C12). Projection of lineage marker tdTomato onto the t-SNE map further revealed that 4 clusters (C2, C6, C7 and C9) were likely derived from NG2-CreER labeled cells and/or their progeny Conclusions: scRNA-seq suggests that tumor OPCs in adult OPC-originated gliomas may function as TICs given their strong stemness feature. Overall design: Glioma cells from genetic mouse model were generated by ScRNA sequencing,single cells were processed through the 10X Chromium 5' (for the primary tumor sample) or 3' (for all cell lines) Single Cell Platform using the Chromium™ Single Cell 5' or 3' Reagent Kits v3 , Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer's protocol (Illumina).