Oncorhynchus mykiss
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR127912_1.fastq.gz | Fastqsanger.gz | |||
| DRR127912_2.fastq.gz | Fastqsanger.gz | |||
| DRR127913_1.fastq.gz | Fastqsanger.gz | |||
| DRR127913_2.fastq.gz | Fastqsanger.gz | |||
| DRR127914_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Objective: Interstitial lung diseases (ILDs) secondary to anti-synthetase syndrome (ASS) greatly influence the prognoses of patients with ASS. Here we aimed to investigate the peripheral immune responses to understand the pathogenesis of this condition. Methods: We performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from 5 patients with ASS-ILD and 3 healthy donors (HDs). Flow cytometry of PBMCs was performed to replenish the results of scRNA-seq. Results: We used scRNA-seq to depict a high-resolution visualization of cellular landscape in PBMCs from patients with ASS-ILD. Patients showed upregulated interferon responses among all cell types. And the ratio of effector memory CD8 T cells to naïve CD8 T cells was significantly higher than that in HDs. Additionally, Th1, Th2, and Th17 cell differentiation signaling pathways were enriched in T cells, and antigen processing and presentation was enhanced in NK cells. Flow cytometry analyses showed increased proportions of Th17 cells and Th2 cells, and decreased proportion of Th1 cells in patients with ASS-ILD when compared with HDs. Conclusions: Our study reveals that ASS-ILD is characterized by upregulated interferon responses, altered CD8 T cell homeostasis, involvement of differentiation signaling pathways of CD4 T cells, and enhanced antigen processing and presentation ability in NK cells by scRNA-seq data. And the proportions of Th17 cells and Th2 cells are higher in patients with ASS-ILD than those in HDs using flow cytometry, while the proportion of Th1 cells is lower. These findings may provide foundations of novel therapeutic targets for patients with this condition.
2021-12-10 | GSE190510 | GEO
Project description:A standardized extract of Centella asiatica (ECa 233) strengthened the hippocampal synapses, resulting in the memory-enhancing effect. The ratio of the major active compounds in the extract – madecassoside [MDS] and asiaticoside [ASS] – is at 1.5 ± 0.5:1. However, the interactions between MDS and ASS are still unknown. To delineate the role of MDS and ASS in ECa 233 on synaptic enhancement by mimicking the applied MDS and ASS concentrations in ECa 233. The hippocampal slices obtained from healthy 8-week-old male Wistar rats and differentiated SH-SY5Y cells were treated with DMSO, ECa 233, MDS, ASS, or MDS+ASS. The hippocampal long-term potentiation (LTP was monitored for 3 h. The cell extracted proteins were examined by proteomic analysis. ECa 233 demonstrated the highest hippocampal synaptic response, followed by the MDS+ASS and the MDS, which expressed a stronger synaptic enhancement effect than the ASS. A number of mitochondrial proteins, including NDUFB6, were also expressed in the differentiated SH-SY5Y cells after treatment with ECa 233, ASS, MDS, and MDS+ASS. Our data revealed that the synergistic effect of MDS and ASS in the combined treatment was necessary to achieve the same level of responses obtained from ECa 233 treatment. MDS majorly contributed to the synaptic enhancement action of ECa 233. In addition, all substances were involved in mitochondrial metabolism, a process necessary for providing energy and sustaining synaptic Ca2+ levels in synaptic transmission. This discovery is crucial for dementia drug development because it demonstrated the role of major parent compounds in ECa 233 and their interaction.
2025-08-13 | PXD057572 | Pride
Project description:Background: A 58-year-old male with anti-synthetase syndrome-associated interstitial lung disease (ASS-ILD) underwent bilateral lung transplantation (LTx) but experienced ILD progression and myositis worsening 38 weeks post-transplant, despite glucocorticoids, tacrolimus, and mycophenolic acid treatment. High-dose glucocorticoids led to adverse effects and ILD exacerbation upon tapering. Objective: To identify persistent inflammatory pathways despite anti-rejection therapy. Methods: Two sets of single-cell RNA-seq (scRNA-seq) analyses were conducted on peripheral blood mononuclear cells (PBMCs) from our patient who experienced recurrent ASS-ILD following bilateral LTx: one before regimen adjustment and one after. The goal these analyses is to investigate systemic inflammatory profiles. Results: In comparison to five ASS-ILD patients without LTx, our patient following bilateral LTx (before regimen adjustment) displayed a higher proportion of CD14⁺ and CD16⁺ monocytes, alongside reduced T, B, and NK cells. Notably, interferon- and JAK-STAT–associated pathways were significantly enriched, as evidenced by marked up-regulation of key genes (e.g. JAK1, JAK2, STAT1, STAT2, STAT3, IL4R, IL6R) in the patient’s monocytes. Elevated serum ferritin levels and the enrichment of macrophage and neutrophil activation pathways further underscored hyperactivation of the mononuclear phagocyte system. Due to poor tolerance of high-dose steroids, limited efficacy of tacrolimus and MPA, and the need to manage post-transplant rejection while controlling ASS, the patient’s regimen was modified. Considering the activation of the mononuclear phagocyte system in the patient, tacrolimus was replaced with cyclosporine A, which is more widely used in macrophage activation syndrome (target trough concentration 120-150 ng/ml). Given the significant activation of the interferon and JAK-STAT pathways in the patient’s activated monocytes, we replaced EC-MPS with the Janus kinase inhibitor (JAKi) tofacitinib at 5 mg twice daily. Short-term high-dose glucocorticoids (methylprednisolone 120 mg/d for 3 days) were also administered before rapid tapering. After regimen adjustment, scRNA-seq was conducted again, which indicated a reduction in CD14⁺ and CD16⁺ monocytes, with T, B, and NK cells rebounding. Neutrophils, characterized by high S100A8, S100A9, and DEFA3 expression, became more prominent. Interferon-related gene expression decreased in monocytes and neutrophils, indicating successful suppression of the interferon pathway. Conclusions: We presented a complicated case of a patient with early recurrence of underlying ASS-ILD after bilateral lung transplantation. We used two sets of scRNA-seq analyses to investigate the systemic inflammatory responses.
2025-01-09 | GSE286228 | GEO
Project description:Agarwood is an expensive resinous heartwood derived from the wounded Aquilaria plants. To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, a handful of transcription factors, and protein kinases related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being M-NM-4-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation. healthy and wounded stems of three-year-old A. sinensis trees
2013-12-31 | E-GEOD-42246 | biostudies-arrayexpress
Project description:Proteomic analysis of antigen-specific serum IgG repertoires from healthy adults vaccinated with either mRNA-1010 or Fluarix quadrivalent influenza vaccines. Serum IgG was characterized using Ig-Seq, an approach integrating immunoglobulin proteomics with B cell receptor sequencing to identify and quantify individual clonotypes comprising the A/H3-specific serological repertoire across multiple time points post-vaccination.
2026-06-03 | PXD077942 | Pride
Project description:Accurately assigning antigen specificity to T cell receptor (TCR) sequences is challenging due to the complexity of the TCR-antigen recognition process in humans. We developed the Peptide-Driven Identification of TCRs (PDI-TCR) assay, a novel method combining in vitro expansion with peptide pools, bulk TCR sequencing, and statistical analysis to identify antigen-specific TCRs from human blood. A key feature of PDI-TCR is its ability to account for bystander T cell expansion using both antigen-specific and non-specific peptide pools, distinguishing true antigen-specific TCRs from the unspecific ones. We applied PDI-TCR to Tuberculosis (TB) patients, sampling blood at diagnosis and throughout therapy, and Mycobacterium tuberculosis (Mtb)-sensitized healthy individuals (IGRA+). We identified hundreds of Mtb-specific and unspecific TCRs, and in combination with single-cell mRNA and TCR sequencing of CD4 T cells, we characterized the transcriptome of Mtb-specific and unspecific T cells in each cohort. Mtb-specific T cells were highly diverse, with the presence of short-lived effector phenotypes only in TB at diagnosis and memory phenotypes maintained through treatment. In contrast, unspecific T cells were more clonally restricted and expanded, cytotoxic, and maintained through treatment. Thus, PDI-TCR is a powerful tool for identifying antigen-specific TCRs. Combined with single-cell sequencing of T cell populations, it enables direct ex vivo monitoring of antigen-specific T cells.
2025-04-30 | GSE293807 | GEO
Project description:we used next-generation sequencing technology to characterize mRNA-seq of Cloeon viridulum (Ephemeroptera: Baetidae) among the young larva (YL), mature larva (ML), subimago (SI), imago (IM) stages, and mixture sampling (composite group, CG).
2018-06-01 | GSE101395 | GEO
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples in two equid species: Somali wild ass and Grevy's zebra. n=12 blood samples
2021-11-25 | GSE184222 | GEO
Project description:Kilian2024 - Immune cell dynamics in Cue-Induced Extended Human Colitis Model
Single-cell technologies such as scRNA-seq and flow cytometry provide critical insights into immune cell behavior in inflammatory bowel disease (IBD). However, integrating these datasets into computational models for dynamic analysis remains challenging. Here, Kilian et al., (2024) developed a deterministic ODE-based model that incorporates these technologies to study immune cell population changes in murine colitis. The model parameters were optimized to fit experimental data, ensuring an accurate representation of immune cell behavior over time. It was then validated by comparing simulations with experimental data using Pearson’s correlation and further tested on independent datasets to confirm its robustness. Additionally, the model was applied to clinical bulk RNA-seq data from human IBD patients, providing valuable insights into immune system dynamics and potential therapeutic strategies.
Figure 4c, obtained from the simulation of human colitis model is highlighted here.
This model is described in the article:
Kilian, C., Ulrich, H., Zouboulis, V.A. et al. Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease. npj Syst Biol Appl 10, 69 (2024). https://doi.org/10.1038/s41540-024-00395-9
Abstract:
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of immunological processes. Despite their high throughput, however, these measurements represent only a snapshot in time. Here, we explore how longitudinal single-cell-based datasets can be used for deterministic ordinary differential equation (ODE)-based modelling to mechanistically describe immune dynamics. We derived longitudinal changes in cell numbers of colonic cell types during inflammatory bowel disease (IBD) from flow cytometry and scRNA-seq data of murine colitis using ODE-based models. Our mathematical model generalised well across different protocols and experimental techniques, and we hypothesised that the estimated model parameters reflect biological processes. We validated this prediction of cellular turnover rates with KI-67 staining and with gene expression information from the scRNA-seq data not used for model fitting. Finally, we tested the translational relevance of the mathematical model by deconvolution of longitudinal bulk mRNA-sequencing data from a cohort of human IBD patients treated with olamkicept. We found that neutrophil depletion may contribute to IBD patients entering remission. The predictive power of IBD deterministic modelling highlights its potential to advance our understanding of immune dynamics in health and disease.
This model was curated during the Hackathon hosted by BioMed X GmbH in 2024.
2025-03-07 | MODEL2502180001 | BioModels