Project description: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
Project description:To study how targeting Glut1 in CAFs influences the transcritome of adjacent cancer cells, MC38 adjacent to control CAFs and Glut1-deficient CAFs were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP
Project description:To study how targeting CMTM6 in CRCs influences the transcritome. Adjacents CAFs of Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP
Project description:To study how targeting Glut1 influences the transcriptome of cancer-associated fibroblasts (CAFs), the transcriptome of control CAFs and that of Glut1-deficient CAFs on murine MC38 liver metastasis sections were obtained and compared with the NanoString GeoMx DSP
Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.
Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.
Project description:Tissue samples from human induced pluripotent stem cell-derived intestinal tissue (iPSC-derived intestinal progenitors seeded onto collagen hydrogels) which were transplanted subcutaneously in mice. Mice were sacrificed and tissues were collected after 2, 3 or 4 weeks following engraftment. The tissues were sectioned onto slides and then profiled using NanoString GeoMX DSP (cancer transcriptome atlas). Normal human colon tissue was also profiled as a reference. In both cases, slides were stained for nuclei and cytokeratin. ROIs were selected from in vivo tissue to represent the entire tissue present. For colon reference tissue, crypt apices and bases were selected. Automated segmentation of each ROI using cytokeratin status (positive / negative) was also performed. Gene expression of all genes was evaluated to determine the most differentially expressed (for reference data). These genes and other intestinal genes were specifically investigated further on in vivo samples to ascertain areas of similarity to adult colon and furthermore to demonstrate maturation across timepoints.
