Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746267 | ENA |
REPOSITORIES: ENA
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Project description:Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired heavy- and light- chain of immunoglobulins (Ig) and VDJ- and VJ- chains of T cell receptors (TCR) from thousands of single cells simultaneously. Due to the complexity of these polyclonal receptors, for many species single-cell immune repertoire sequencing assays are not yet commercially available. Rhesus macaques are one of the most well-studied model organisms of the human adaptive immune response; application of these new immune repertoire sequencing assays is highly relevant to vaccine and infectious disease studies. Here we use custom designed primers to target and enrich for every known Ig and TCR chain and isotype in the rhesus macaque animal model. We sequenced more than 110,000 cell barcodes from rhesus macaque repertoires using PBMC, splenocyte, and FACS-sorted T and B cell. We were able to recover every Ig and TCR isotype, measure clonal expansion in proliferating T cells, and pair repertoires with gene expression profiles of single cells. Our results establish the ability to perform single-cell based immune repertoire analysis in rhesus macaque.
2021-11-18 | GSE179722 | GEO
Project description:High-throughput Ig and TCR repertoire single-cell sequencing analysis in rhesus macaques
| PRJNA744766 | ENA
Project description:HLA-E molecules can present self and pathogen-derived peptides to both NK-cells and T-cells. T-cells that recognize HLA-E peptides via their T-cell receptor (TCR) are termed donor-unrestricted T-cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T-cells from 21 individuals recognizing HLA-E tetramers (TM) folded with 2 Mtb HLA-E restricted peptides. We sorted HLA-E Mtb TM+ and TMCD8+ T-cells directly ex vivo and performed bulk RNA-sequencing and single cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E Mtb specific T-cells have a highly diverse TCR repertoire.
2024-02-04 | GSE236154 | GEO
Project description:By using 10X genomics single-cell RNA sequencing plat, we employed malignant pleural effusion as research model to performed single-cell RNA sequencing to map the immune microenvironment of MPE. Meanwhile we performed TCR and BCR sequencing for immune receptor repertoire analysis.
2021-10-15 | GSE185058 | GEO
Project description:To explore the role of Satb1 in rearrangement and repertoire of TCR genes, we used Satb1contional knockout micwhich the Satb1 gene was deleted in long term hematopoietic stem cells. We applied 5ʹRACE (rapid amplification of cDNA ends) PCR technique to generate deep sequencing libraries of Tcrd, Tcrg, Tcrb, and Tcra cDNA by using a single set of primers for each TCR gene. We obtained millions of TCR sequences and unraveled the complexity of T-cell diversity. Our experimental evidence demonstrates that Satb1 has substantial influences on the TCR repertoire.
2020-07-10 | GSE154069 | GEO
Project description:Considerable progress has recently been made in cancer immunotherapy, including immune checkpoint blockade, cancer vaccine, and adoptive T cell methods. The lack of effective targets is a major cause of the low immunotherapy response rate in colorectal cancer (CRC). Here, we used a proteogenomic strategy comprising immunopeptidomics, whole exome sequencing, and 16S ribosomal DNA sequencing analyses of 8 patients with CRC to identify neoantigens and bacterial immunopeptides that can serve as antitumor targets. This study directly identified several personalized neoantigens and bacterial immunopeptides. Immunoassays showed that all neoantigens and 5 of 8 bacterial immunopeptides could be recognized by autologous T cells. Additionally, T cell receptor (TCR) αβ sequencing revealed the TCR repertoire of epitope-reactive CD8+ T cells. Functional studies showed that T cell receptor -T (TCR-T) could be activated by epitope pulsed lymphoblastoid cells. Overall, this study comprehensively profiled the CRC immunopeptidome, revealing several neoantigens and bacterial immunopeptides with potential to serve as immunotherapy targets in CRC.
2023-11-28 | PXD047311 | iProX
Project description:Conventional CD4 and CD8 single positive T cell lineages constitute the main differentiation pathway in the thymus. In human thymus, a minor TCRαβ differentiation pathway diverges from the early double positive stage, consisting of CD10+ PD-1+ cells. These cells are phenotypically and functionally similar to murine agonist-selected intraepithelial T lymphocyte precursors (IELps) which home to the small intestine. Here, the progeny of the human agonist-selected IEL lineage was identified in antigen-inexperienced cord blood (CB) with a polyclonal T cell receptor (TCR) repertoire exhibiting a bias towards early TCR alpha chain rearrangements and elevated autoreactive indices. Single-cell RNA sequencing allowed further delineation of this unconventional lineage in CB. Trajectory analysis, along with TCR repertoire analysis, transcriptomics and proteomics, suggests a precursor-progeny relationship with the thymic IELps. The distinct, heterogeneous CB population can now be defined as CD3+ TCRαβ+ CD4- CCR7- CD26-. Besides recent thymic emigrants, this population also consists of newly identified effector clusters and previously described populations: the suppressive NK receptor expressing CD8+ Treg population, the KIR/NKG2A+ EOMES+ virtual memory population and the CD8αα+ T cell populations. The population shows a discriminating stable HELIOS expression and is exclusively able to downregulate CD8β expression, resulting in double negative T cells. The functional properties of this population suggest that the cells expand on inflammatory cues and exert cytotoxic and proinflammatory activity.
2023-02-10 | PXD033392 | Pride
Project description:To illustrate the immune cell atlas and functional heterogeneity of T cell repertoire in murine heart transplantation，we established the murine heterotopic heart transplantation model and isolated CD45 positive cells from cardiac grafts and spleens for single cell transcriptome and TCR sequencing.
2024-01-06 | GSE249989 | GEO
Project description:The data corresponds to the analysis of T cell receptor (TCR) repertoires of FACS-purified Tstem, Tpex and TEM cells of six individuals. The analysis of the TCR beta chain (TRB) demonstrated the differences between Tstem and Tpex repertoire properties. In total, 36 samples were analyzed using the Human TCR Profiling Kit (MiLaboratory LLC) for sequencing libraries preparation and Illumina NextSeq 550 sequencing (150+150bp) followed by the demultiplexing procedure using MIGEC software.
2020-08-01 | E-MTAB-8892 | biostudies-arrayexpress
Project description:We used 454 sequencing to assess the repertoire of B cell subsets from bone marrow, spleen, and small intestinal lamina propria from two mouse strains. We used a RAG2-GFP reporter mouse strain (129Sve background) to isolate CD19+ RAG2+ B lineage cells from bone marrow and small intestinal lamina propria and total splenic B cells. We used 5' RACE to amplify cDNA libraries using primers specific for the mu constant region of IgH and the Ig kappa constant region. We also used this technique to analyze total B cell libraries from Swiss Webster germ-free mice to compare to littermate controls that were cohoused with regular specific pathogen free (SPF) mice for 7 days. Examination of the Ig kappa repertoire and IgH repertoire in RAG2+ bone marrow B lineage cells compared to RAG2+ small intestinal lamina propria B lineage cells or total splenic B cells. There are 8 (Ig kappa) or 4 (IgH) independent experiments comparing repertoires in RAG2-GFP mice. Each experiment in RAG2-GFP+ mice consisted of a pool of 8-12 mice. There are 3 experiments comparing germ-free to colonized mouse total B cell repertoires, each consisting of one mouse per condition.
2013-07-16 | E-GEOD-48870 | biostudies-arrayexpress