Single-cell RNA-seq profiling of sgNTC control and sgDnmt3a knockout MC38 mouse tumor tissues

We performed single-cell RNA sequencing on MC38 tumor tissues from the sgNTC control group and the sgDnmt3a knockout group. Single-cell suspensions were prepared from enzymatically digested tumor tissues, and scRNA-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3.

Libraries were sequenced on the Illumina NovaSeq 6000 platform. Raw FASTQ files were processed with Cell Ranger v8.0.1, aligned to the GRCm39 mouse reference genome, and unique molecular identifier (UMI) count matrices were generated for each cell barcode. Downstream analyses including quality control, highly variable gene identification, dimensionality reduction and cell clustering were performed using the Seurat R package (v4.0.0).