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 Overall design: 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.