Project description:The degenerative process in Parkinson’s disease (PD) causes a progressive loss of dopaminergic neurons (DaNs) in the nigrostriatal system. Resolving the differences in neuronal susceptibility warrants an amenable PD model that, in comparison to post-mortem human specimens, controls for environmental and genetic differences in PD pathogenesis. At present study, we generated a primate model of PD by carotid artery injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine MPTP and sampled substantia nigra and putamen of macaque for single cell sequencing analysis.
Project description:To goal of the experiment is to assess whether we can profile enough cells corresponding to the host TME. In this PDX model, most of the cells correspond to the xenograft material, with limited amounts of host TME cells. To this aim we loaded 16 times more cells hybridized with the mouse probe set compared to the human hybridization.
Project description:The goal of the experiment is to determine whether it is feasible to use the 10x Genomics Gene Expression Flex solution in samples containing a mixture of human and mouse cells. First we tested how the presence of mouse cells impacted the data recovered by the use of the human whole trasnscriptome amplification (WTA) probe sets. Then we profiled a mixed species sample by using human and mouse probe sets in the same reaction. Finally, for samples with lower amounts of human cells we tried to correct the amount of cells recovered by the human and mouse probe sets by adjusting the amount of cells loaded from the respective hybridizations.
Project description:Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. SUM159PT cells infected with a lentiviral barcode library (Perturb-seq Library) were sorted according to the presence of BFP signal, treated or not with paclitaxel (PTX), and then processed by scRNA-Seq or Multiome.
Project description:The goal of the experiment is determine whether the mixing of human and mouse probe sets of the 10x Genomics Gene Expression Flex allows to profile cell line derived xenograft (CDX) samples. We profiled a CDX vehicle sample and a CDX sample after 10 days of treatment with Osimertinib at 25mg/kg.
Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.
Project description:Naive B cells (CD27-IgD+) were obtained from 3 healthy controls and cultured in vitro under anti-IgM, CD40L and IFN-gamma to polarise class-switching towards IgG isotypes. Single-cell RNA and BCR sequencing libraries were prepared at Day 0 (before addition of stimuli), Day 3 and Day 6 of the cell culture time-course. This is intended as a dataset to validate a new computational method sciCSR in enumerating productive and sterile immunoglobulin transcripts as indicators of B cell class switching and maturation dynamics.