Similar Datasets
Project description:RNA sequencing of human CD8+ T cell subsets [MEM]
| PRJNA980109 | ENA
Project description:Gene expression profiling has opened new directions of investigation in scientific research, however, the need for substantial amount of biological material to perform these experiments limits significantly its application range. Here, we have developed procedures to perform microarray analysis on amplified cDNA from single cells, including primary T lymphocytes, and applied this technology to the study of CD4 and CD8 lineage differentiation. Gene expression profiling was performed on samples of 1000 cells from 10 different subpopulations, defining the major stages of post-thymic CD4+ or CD8+ T-cell differentiation. Surprisingly, our data revealed that while CD4+ and CD8+ T-cells evolve differently at early stages of differentiation, they become increasingly similar as they reach late differentiation stages. This suggests that the functional heterogeneity of antigen experienced CD4+ and CD8+ T-cells is located early during post-thymic differentiation, and that late stages of differentiation may represent a common end in the development of T-lymphocytes. Keywords: Gene expression profiling
2007-06-30 | GSE6732 | GEO
Project description:We isolated highly purified CD8+CD28+ and CD8+CD28- T cell populations from healthy young and elderly persons for gene expression profiling using Affymetrix oligonucleotide microarrays. We demonstrate that the gene expression profile of CD8+CD28- T cells is very similar in young and elderly persons. In contrast, CD8+CD28+ in elderly differ from CD8+CD28+ in young persons. Hierarchical clustering revealed that CD8+CD28+ in elderly are located between CD8+CD28+ in young and CD8?CD28- (young and old) T cells regarding their differentiation state. Our study demonstrates a dichotomy of gene expression levels between CD8+CD28+ T cells in young and elderly persons but a similarity between CD8+CD28- T cells in young and elderly persons. As CD8+CD28+ T cells from elderly and young persons are distinct due to a different composition of the population, these results suggest that the gene expression profile does not depend on chronological age but depends on the differentiation state of the individual cell types.
2010-09-03 | E-MEXP-2345 | biostudies-arrayexpress
Project description:Cytotoxic CD8+ T cells can effectively kill target cells by producing cytokines, chemokines and granzymes. Expression of these effector molecules is however highly divergent, and tools that identify and pre-select potent killer cells are lacking. Human CD8+ T cells can be divided into IFNGand IL-2 producing cells. Unbiased RNA-sequencing and proteomics analysis on cytokine-producing fixed CD8+ T cells revealed that IL-2+ T cells produce helper cytokines, and that IFNG+ T cells produce cytotoxic molecules. IFNG+ cytotoxic T cells expressed the surface marker CD29 already prior to stimulation. CD29 also marked T cells with cytotoxic gene expression from different tissues in single-cell RNA-sequencing data. Notably, the cytotoxic features of CD29+ T cells were maintained during cell culture, suggesting a stable phenotype. Pre-selecting CD29-expressing MART1 TCR-engineered T cells potentiated the killing of target cells. We therefore propose that selecting for CD29+ T cells could boost the anti-tumoral activity of T cell therapeutics.
2021-09-08 | PXD012874 | Pride
Project description:The presented data corresponds to the analysis of two discrete subsets of human CD8+ naive T cells, defined by positive and negative expression of the chemokine receptor CXCR3 (TNR3-, TNR3+). In this study we demonstrated that these subsets have different potential to generate fully-differentiated effector T cells following antigen-specific stimulation. The performed systematic immune repertoire analysis (T cell receptor beta chain (TRB)) of the sorted cell subsets revealed diverse physico-chemical properties of TRB CDR3 sequences suggesting enhanced TCR self-reactivity in human TNR3+ cells. In total, we analyzed 74 samples (from 11 patients, 3 replicates of each cell subset (excluding one missing replicate) and additionally for 3 patients CD8+ memory T cells in 3 replicates). We used 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 (https://github.com/mikessh/migec).
2019-10-17 | E-MTAB-7638 | biostudies-arrayexpress
Project description:Transcriptional profiling of mouse in-vitro derived CD8+ cells (obtained after culturing BM-HSCs isolated from B6 mice) with OP9-DL1 cells for 35 days were compared to CD8+ thymocytes isolated from 4-5 weeks old B6 mice. Our goal was to determine similarities and differences in gene expression profile between in vitro-derived CD8+ cells and CD8+ cells isolated from the thymus. The procedure of in vitro differentiation of HSC using OP9-DL1 cocultures was previously described by: Schmitt, T. M., and J. C. Zuniga-Pflucker. 2002. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17:749-756 and Holmes, R., and J. C. Zuniga-Pflucker. 2009. The OP9-DL1 system: generation of T-lymphocytes from embryonic or hematopoietic stem cells in vitro. Cold Spring Harb Protoc 2009:pdb prot5156. Biological replicates: 2 different samples of in vitro-derived CD8+ T cells from day 35 were compared to 2 different samples of thymic CD8+ cells.
2012-09-05 | E-GEOD-37669 | biostudies-arrayexpress
Project description:RNA sequencing of human CD8+ T cell subsets to compare hypofunctional exhausted cells (TEX) to fully activated effector cells (TEFF).
2023-07-01 | GSE234100 | GEO
Project description:Antigen recognition by CD8+ naïve T cells induces immune activation and rapid effector differentiation that ensures elimination of virally-infected and malignant cells. While signals from the extracellular milieu and downstream of the TCR have long been known to play a crucial role, it is currently unknown whether heterogeneity within the naïve CD8+ T cell pool shapes the potency of effector differentiation. We report the identification of two discrete subsets of human CD8+ TN cells, defined by positive and negative expression of the chemokine receptor CXCR3, with different potential to generate fully-differentiated effector T cells following antigen-specific stimulation. The CXCR3+ are more abundant than the CXCR3– naïve in peripheral blood and lymphoid tissues, retain enhanced expression of effector-related genes ex vivo and display features of the T cell receptor chain repertoire indicating enhanced capacity to bind the peptide:major histocompatibility complex. Likewise, a phenotypically equivalent murine CD8+ naïve population expressing high levels of CD5, a surrogate indicator of enhanced TCR sensitivity for self, preferentially generates short-lived effector cells following infection. Our findings imply that CD8+ T cell effector differentiation potential in humans is shaped by heterogeneity in the preimmune repertoire
2019-10-17 | GSE125100 | GEO
Project description:Analyzing and comparing proteome and phosphoproteome profiling between CD8+ DC and CD8- DC not only will be very helpful to understand the molecular mechanisms regulating CD8+/- DC differentiation and function but also can screen CD8+ or CD8- DC specific regulatory pathways or molecules.
2018-06-11 | PXD006875 | Pride
Project description:Antigen recognition by CD8+ naïve T cells induces immune activation and rapid effector differentiation that ensures elimination of virally-infected and malignant cells. While signals from the extracellular milieu and downstream of the TCR have long been known to play a crucial role, it is currently unknown whether heterogeneity within the naïve CD8+ T cell pool shapes the potency of effector differentiation. We report the identification of two discrete subsets of human CD8+ TN cells, defined by positive and negative expression of the chemokine receptor CXCR3, with different potential to generate fully-differentiated effector T cells following antigen-specific stimulation. The CXCR3+ are more abundant than the CXCR3– naïve in peripheral blood and lymphoid tissues, retain enhanced expression of effector-related genes ex vivo and display features of the T cell receptor chain repertoire indicating enhanced capacity to bind the peptide:major histocompatibility complex. Likewise, a phenotypically equivalent murine CD8+ naïve population expressing high levels of CD5, a surrogate indicator of enhanced TCR sensitivity for self, preferentially generates short-lived effector cells following infection. Our findings imply that CD8+ T cell effector differentiation potential in humans is shaped by heterogeneity in the preimmune repertoire
2019-10-17 | GSE125099 | GEO