Ontology highlight
ABSTRACT:
PROVIDER: PRJNA491919 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7878370_1.fastq.gz | Fastqsanger.gz | |||
| SRR7878370_2.fastq.gz | Fastqsanger.gz | |||
| SRR7878380_1.fastq.gz | Fastqsanger.gz | |||
| SRR7878380_2.fastq.gz | Fastqsanger.gz | |||
| SRR7878390_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 56 |
Similar Datasets
Project description:Single-cell transcriptomic profiling was performed on FACS-enriched peripheral blood gamma-delta T cells from three healthy donors and three patients with plaque psoriasis. The study defines circulating gamma-delta T-cell states and disease-associated remodeling, including a shift toward late effector polarization and reduction of a CSMD1-marked state.
2026-09-01 | GSE335977 | GEO
Project description:Here we compare the transcriptional profile of HMB-PP-stimulated versus OKT-3 stimulated human peripheral blood gamma-delta T cells. We show that HMB-PP faithfully reproduces the transcriptional events associated with bona fide activation through the T cell receptor (TCR).
2008-09-01 | E-MEXP-1601 | biostudies-arrayexpress
Project description:High-throughput sequencing (HTS) of antibody amplicon libraries has become a powerful method in the emerging field of systems immunology. However, numerous sources of bias in HTS workflows may affect antibody repertoire data. A crucial step in antibody amplicon library preparation is the addition of adapter sequences, which are platform-specific short nucleotide sequences. In addition to conventional ligation-based adapter addition, it is also possible to use PCR-based methods such as Direct Addition (one-step adapter addition, DA) and Primer Extension (two-step adapter addition, PE), which have led to the lack of a consensus method and uncertainty regarding the impact of adapter addition on repertoire HTS data. Therefore, we compared all three methods by performing HTS with the Illumina MiSeq platform using total RNA originating from mouse antibody-secreting cells. We used technical replicate-based validation and clonal overlap and rank statistics to demonstrate that the two PCR-based methods produced HTS repertoires equivalent to ligation. Specifically: Nine BALB/c mice (8-10 weeks old, Charles River, specific-pathogen free) were immunized with 50 ug alum-precipitated chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl (NP, NP-CGG, BioCat). Mice were sacrificed 14 days post-immunization (dpi) and their spleens and bone marrow (from femurs and tibia) were harvested. Antibody-secreting CD138-positive cells were enriched from spleen and bone marrow 14 dpi as previously described (Reddy, 2010, Nat Biotech).
2014-02-20 | E-MTAB-2226 | biostudies-arrayexpress
Project description:Background: Malignant clones of primary cutaneous T-cell lymphomas (CTCL) can show a CD4+, CD8+ or T-cell receptor γδ+ phenotype, but their individual impact on tumor biology and skin lesion formation remains ill-defined. We perform a comprehensive molecular characterization of CD4+ vs. CD8+ and TCR-γ/δ+ CTCL lesions. Methods: We performed scRNA-seq of 18 CTCL skin biopsies to compare classic CD4+ advanced-stage mycosis fungoides (MF) with TCR-γ/δ+ MF and primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (Berti’s lymphoma). Results: Malignant clones of TCR-γ/δ+ MF and Berti’s lymphoma showed similar clustering patterns distinct from CD4+ MF, along with increased expression of cytotoxic markers such as NKG7, CTSW, GZMA, and GZMM. Only advanced-stage CD4+MF clones expressed central memory T-cell markers (SELL, CCR7, LEF1), alongside B1/B2 blood involvement, whereas TCR-γ/δ+ MF and Berti’s lymphoma harbored a more tissue-resident phenotype (CD69, CXCR4, NR4A1) without detectable cells in the blood. CD4+ MF and TCR-γ/δ+ MF skin lesions harbored strong type 2 immune activation across myeloid cells, while Berti’s lymphoma was more skewed towards type 1 immune responses. Both CD4+ MF and TCR-γ/δ+ MF lesions showed upregulation of keratinocyte hyperactivation markers such as S100As and KRT16 genes. This increase was entirely absent in Berti’s lymphoma, possibly reflecting an aberrant keratinocyte response to invading tumor cells, that could contribute to the formation of the typical ulcero-necrotic lesions within this entity. Conclusions: Our scRNAseq profiling study reveals specific molecular patterns associated with distinct CTCL subtypes.
2024-10-24 | GSE266862 | GEO
Project description:The Ag receptors on alpha/beta and gamma/delta T cells differ not only in the nature of the ligands that they recognize but also in their signaling potential. We hypothesized that the differences in alpha/beta - and gamma/delta TCR signal transduction were due to differences in the intracellular signaling pathways coupled to these two TCRs. To investigate this, we employed transcriptional profiling to identify genes encoding signaling molecules that are differentially expressed in mature alpha/beta and gamma/delta T cell populations. Unexpectedly, we found that B lymphoid kinase (Blk), a Src family kinase expressed primarily in B cells, is expressed in gamma/delta T cells but not in alpha/beta T cells. Analysis of Blk-deficient mice revealed that Blk is required for the development of IL-17-producing gamma/delta T cells. Furthermore, Blk is expressed in lymphoid precursors and, in this capacity, plays a role in regulating thymus cellularity during ontogeny. Naive alpha/beta and gamma/delta T cells isolated from mouse lymph nodes and purified by negative selection were compared using MOE430 2.0 GeneChip.
2010-09-23 | E-GEOD-24281 | biostudies-arrayexpress
Project description:We performed gene expression profiling in 34 peripheral T-cell lymphoma, including 7 cases of gamma delta T-cell lymphoma to identify a unique T-cell receptor signature gene set for classification of gamma delta T-cell lymphoma and alpha beta T-cell lymphoma.
2008-10-15 | GSE11946 | GEO
Project description:B cells are crucial players in the pathogenesis of multiple sclerosis (MS), however, limited information is available on peripheral immunoglobulin (Ig) repertoires of people with MS (pwMS) in comparison to healthy individuals and during different treatments. Next generation sequencing of Ig heavy chains (VH) originating from bulk-sorted B cell populations was performed in 33 pwMS and ten healthy controls. All 33 pwMS were examined longitudinally at baseline and six months after treatment with ozanimod, fingolimod, dimethyl fumarate, teriflunomide, cladribine or natalizumab. Ig peptides were obtained longitudinally in a subset of treated pwMS by Ig mass spectrometry, overlapped with VH transcriptomes through nf-core bioinformatics workflow analysis and additionally Ig serum level and anti-Epstein-Barr virus IgG level (EBNA1) were measured. VH repertoires of treatment-naïve pwMS showed a significantly decreased diversity in the double negative B cells and different usage of IGHV genes when compared with healthy controls. Quantitative changes in B cell subsets during treatment were accompanied by qualitative changes in Ig repertoires with a significantly decreased diversity in the naive, memory B cells and plasmablasts during ozanimod treatment. A similar trend was noticeable for all other treatments except natalizumab. No qualitative change in Ig peptides overlapping with Ig transcriptome repertoires was observed. This study provides first evidence for an altered peripheral Ig repertoire in pwMS. In addition, various treatments seem to shift the composition of B cells towards an increased fraction and activation of the naive B cell pool and a reduced fraction of memory B cells with reduced clonal diversity.
2026-04-27 | PXD075641 | Pride
Project description:Tissue injury responses are governed by dynamic immune-stromal crosstalk that can promote productive tissue repair or drive dysregulated extracellular matrix (ECM) production and aberrant vascular remodeling, culminating in fibrosis. Here, we investigate how gamma T cells interact with stromal cells to shape tissue fibrosis using a preclinical model of the biomaterial foreign body response that induces a reproducible, dense fibrotic encapsulation. A mixed population of tissue-resident and migratory gamma delta T cells, consisting of type-1 (gamma delta IFN gamma) and multiple type-17 (gamma delta 17) effector subsets, accumulated at the biomaterial implantation site during the early inflammatory phase of wound healing. While the gamma delta IFN gamma later contracted as tissue fibrosis progressed, the activated gamma delta 17 persisted and served as a dominant source of interleukin (IL)-17. Aging and exposure to a high-fat diet, both factors associated with chronic inflammation and pathological fibrosis, further heightened the gamma delta 17 response. The gamma delta 17 secreted bioactive factors that stimulated fibroblast expression of pro-inflammatory and collagen genes in a Transwell co-culture assay. Computational inference of intercellular communication further linked cytokines and growth factors expressed by gamma delta T cells to the activation of fibroblast and endothelial cell transcription factors involved in ECM remodeling and vascular development, respectively. The elimination of gamma delta T cells with a TCR delta knockout strain resulted in differential expression of ECM and skeletal muscle components as well as altered blood vessel structure within the fibrotic matrix. Altogether, our results propose that signaling from gamma delta T cells can affect stromal cell phenotypes, ultimately influencing the composition and vascularity of fibrotic tissue.
2025-06-13 | MSV000098194 | MassIVE
Project description:We used microarrays to detail the global programme of gene expression by circulating TCRVgamma9+ gamma delta T cells isolated from healthy individuals,tested either as resting cells or cells activated by phosphoantigen BrHPP and IL-2at an early(+6hrs) and a late (+7days) timepoint. We find that with more “NK cell” genes than alphabeta T cells and more “T cell” genes than NK cells, the circulating TCRVgamma9+ gamma delta T cells cells have a hybrid transcriptome. The gene signature of the activated cells recapitulates their physiological functions: Th1 cytokine, chemokine and cytotoxic activities at first and mitotic activity at later time points. The gene expression pattern of activated normal gamma delta T cells is nevertheless clearly distinctive from that of NK/T and peripheral T cell lymphomas of the gamma delta subtype.
2011-02-15 | GSE27291 | GEO