Project description:To further explore the transcriptional changes in the kidney transplant biopsy at time of rejection, scRNAseq analysis was performed on 16 kidney transplant biopsy-derived cells using 10X Genomic technology.
Project description:To further explore the transcriptional changes in the peripheral blood leukocytes at time of Antibody-mediated rejection (ABMR), scRNAseq analysis was performed on 12 peripheral blood samples (6 ABMR and 6 stable patients paired for age and time after transplantation) using 10X Genomic technology.
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:To further explore the transcriptional homogeneity of Tet+ cells with high numbers, we performed scRNAseq of FACS-sorted BDC2.5mi/IAg7 and InsB13-21/IAg7 Tet+ and Tconv cells from pMHCII-NP-treated animals, using the 10x Genomics platform. To study the effect of Bcl6-KO, we also studied transcriptional differences between WT and Bcl6-KO a-CD3-induced IL-10-producing T cells
Project description:Live CD45+ cells from the peripheral blood (PB) and synovial tissue (ST) of 3 naive to treatment RA patients were sorted for single cell RNA sequencing (scRNAseq) using 10x Genomics platform. Library preparation was performed using 10X Single Cell 3’ Reagent Kits v2 and libraries were sequenced on the Illumina HiSeq 4000 system to a minimum depth of 50k reads/cell.
