Single cell RNA-sequencing of C134 oHSV-treated murine medulloblastoma

Here, we studied the effects of oHSV C134 in two syngeneic medulloblastoma mouse models, one that aligns with the sonic hedgehog (SHH) subtype (MYCN) and another that aligns with tumors of the group 3 subtype (CMYC).We harvested tumor tissue two and six days post-injection of C134 and performed single cell RNA-sequencing (scRNA-seq). Overall design: To investigate if the second-generation, chimeric HCMV/HSV-1 oncolytic virus C134 (Cassady, 2005, J Virol) is a promising therapeutic treatment for medulloblastoma we utilized two syngeneic mouse medulloblastoma models: one that aligns with the gene expression profile associated with medulloblastoma of the sonic hedgehog subtype (MYCN; Zindy et al., 2007, Cancer Res), and another that aligns with tumors of the Group 3 subtype (CMYC; Kawauchi et al., 2012, Cancer Cell). Tumors were serially transplanted through the brains of mice and treated with either C134 oHSV or vehicle. Tumors were resected 2- and 6- days post-treatment (1 mouse per group, 8 samples total in our experiment). The Chromium Next GEM Single Cell 3' v3.1 single index kit from 10x Genomics was used to carry out cell capture and library preparation. Targeted recovery was 8,000 cells per sample. FASTQs were generated using cellranger (v6.0.0) mkfastq with default parameters. Raw counts were generated by aligning FASTQs to a combined custom reference that included mus musculus + C134 oHSV transcripts using cellranger (v6.0.0) count with default parameters.