Transcriptomic profiling of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

To study how targeting CMTM6 inCRCs influences the transcritome. Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP Two months old C57BL6 mice received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-pan cytokeratin for MC38 cells, and SYTO13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin-) within a same ROI were collected for transcriptomic profiling as well. Segments 1-15 (12 is not included) were ROIs from control MC38 liver metastases and 16-28 were from CMTM6 knockdown MC38 liver metastases. 54 sequencing data were generated for MC38 cancer cells due to dual-indexing primers-based sequencing.