The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell)
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ABSTRACT: Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset only contains the metadata and processed data. Raw data can be accessed via the EGA accession EGAS00001003734
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:The STOPAGO study enrolled adults with persistent or chronic primary immune thrombocytopenia (ITP) and complete response to thrombopoietin receptor agonist (TPO-RA). TPO-RA discontinuation was planned in the study and patients with sustained complete response off-treatment (SCROT, platelet count > 100 G/L and no bleeding) and non sustained response (NSR, platelet count < 30 G/L or bleeding) were identified at week 24. RNAseq of peripheral blood mononuclear cells was performed at baseline, before TPO-RA discontinuation. Samples originated from 8 patients (4 with SCROT and 4 with NSR). The objectif was to identify putative markers that would predict relapses after TPO-RA discontinuation by comparing SCROT and NSR patients.
Project description:Study of the emergence of the rare 2C like cell population upon Retinoic Acid treatment. Transcriptionally characterise the different cell populations emerging at different timepoints upon Retinoic Acid treatment and identify genes driving cell fate decisions.
Project description:This study demonstrates cellular and molecular mechanisms regulating the generation and function of basal radial glia (bRG), a neural stem cell population that was shown to be enriched in the developing human brain and was involved in the formation of cortical expansion. Here, we studied the role of LGALS3BP, a secreted protein whose RNA expression is enriched in bRGs. Based on a combination of three model systems i) in vitro human cerebral organoids, ii) ex vivo embryonic human fetal tissue and iii) in vivo embryonic mouse cortex, and a wide variety of techniques including single-cell RNA-sequencing, proteomics, and immunostaining, we characterized the role of human LGALS3BP mutations.
Project description:We aimed to examine changes in cellular composition of intestinal crypts, villi, and polyps from wild-type, Grem1-overexpressing (Vil1-Grem1) and anti-Grem1 antibody-treated (30 mg/kg subcutaneously weekly from the age of 6-weeks old for 10 weeks) Vil1-Grem1 mice by scRNA-seq. The proximal small bowel was dissected out the muscle layer was scraped off mechanically with a coverslip and discarded. The villus compartment and crypt compartment were separated mechanically and digested into a single cell suspension and processed using a 10X Genomics Chromium Single Cell 3' v3 kit and Chromium Instrument.
Project description:Multi-omics single-cell profiling of surface proteins, gene expression and lymphocyte immune receptors from hospitalised COVID-19 patient peripheral blood immune cells and healthy controls donors. Identification of the coordinated immune cell compositional and state changes in response to SARS-CoV-2 infection or LPS challenge, compared to healthy control immune cells.
Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.
Project description:Bulk RNA-sequencing experiments were performed to analyze the transcriptomic effects of such integrations into two newly established genomic safe harbor sites. Jurkat and HEK293T cells were edited to integrate CMV-mRuby expressing cassette into Rogi2 genomic safe harbor site using Cas9 RNP