Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Wild-type and yellow-mutant Triplophysa siluroides muscle LC-MS

ABSTRACT: WT T. siluroides exhibited significantly higher muscle hardness compared to YM individuals, with consistent trends observed in gumminess and resilience. To investigated muscle quality differences between wild-type (WT) and yellow-mutant (YM) Triplophysa siluroides, the muscle proteomic analyses was conducted.

INSTRUMENT(S):

ORGANISM(S): Triplophysa Siluroides

TISSUE(S): Enteric Muscle

SUBMITTER: Luyun Ni

LAB HEAD: Luyun Ni

PROVIDER: PXD066809 | Pride | 2026-01-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20250429_173126_GDPL23120363-2.sne	Other
	RAW.zip	Other
	checksum.txt	Txt

Items per page:

1 - 3 of 3

Publications

Comparative Muscle Quality and Multiomic Analyses in Wild-Type and Yellow-Mutant Triplophysa siluroides: TGF-β/BMP-Mediated Covariation and Breeding for Muscle Quality.

Ni Luyun L Li Feiyang F Li Pengcheng P Chen Yeyu Y Liu Yan Y Du Jun J Lai Jiansheng J Liu Ya Y

Foods (Basel, Switzerland) 20251206 24

This study investigated muscle quality differences between wild-type (WT) and yellow-mutant (YM) Triplophysa siluroides. Texture analysis showed WT T. siluroides had significantly greater hardness, gumminess, and resilience than YM. Histological and biochemical analyses ruled out myofiber diameter/density as drivers, instead identifying reduced collagen in YM as key, as confirmed by Picrosirius red staining, collagen quantification, and transmission electron microscopy. Transcripto ...[more]

PMID: 41464906

Similar Datasets

Melatonin Rescues Triclosan-Disrupted Porcine Oocyte Meiosis via Suppression of p53-Mediated Apoptosis

Project description:This study investigates the toxic effects of the environmental contaminant triclosan (TCS) on porcine oocyte meiosis and the protective role of melatonin (MT). Using an in vitro maturation model, TCS was found to impair polar body extrusion and cumulus expansion, while inducing oxidative stress, mitochondrial and endoplasmic reticulum dysfunction, and apoptosis. To explore the underlying molecular mechanisms, we performed proteomic profiling using a Bruker timsTOF Pro2 mass spectrometer with a Direct DIA acquisition strategy. Differentially expressed proteins (DEPs) were quantified and analyzed using Spectronaut software, followed by functional annotation and enrichment analysis via GO, KEGG, and Reactome databases. The results revealed that the p53 signaling pathway plays a central role in both TCS-induced toxicity and MT-mediated rescue, providing new insights into reproductive damage caused by environmental pollutants.

2025-11-17 | PXD068303 | Pride

Identification of differentially expressed proteins in mouse testes by LC-MSMS

Project description:Identify the differentially expressed proteins between control and Exosc10 conditional knockout testes.

2025-09-30 | PXD052908 | Pride

Proteomic analysis of the physiological response of high CO2 stimulation tetraploid Robinia pseudoacacia L.

Project description:When plants are continuously treated with high concentration of CO2, they will show different physiological and biochemical characteristics due to the different conditions of the plants themselves and the environment, and the leaves, as the main organ of gas exchange between plants and the outside world, will first respond to CO2 stress through photosynthesis and respiration when the atmospheric concentration of CO2 rises. In this study, tetraploid Sophora japonica was selected as the research object to analyze the stomatal movement pattern and the changes of photosynthesis and respiration under high CO2 culture conditions, and we found that ROS and NO were synthesized and participated in the regulation of CO2-mediated stomatal closure, and we also proved that the alternate respiration pathway could alleviate the oxidative damage caused by high CO2 concentration. Combined with the proteomics approach, the key proteins responsive to high concentration of CO2 were mined according to the changes of differential proteins under different treatment conditions, with the aim of laying a theoretical foundation for the study of elucidating the response mechanism of tetraploid Sophora japonica under high concentration of CO2 treatment.

2024-06-16 | PXD047363 | Pride

Plasma Proteomic Analysis Based on 4D-DIA Evaluates the Clinical Response to Imrecoxib in the Early Treatment of Osteoarthritis

Project description:Nonsteroidal anti-inflammatory drugs (NSAIDs) are the primary treatment for osteoarthritis (OA), but prolonged use has adverse effects and varying efficacy. Among NSAIDs, imrecoxib, a selective cyclooxygenase-2 (COX-2) inhibitor, reduces side effects yet remains ineffective for half the patient population. This study aims to identify biomarkers for early imrecoxib efficacy evaluation in OA for personalized therapy optimization. From September 2021 to January 2022, imrecoxib was administered to patients with OA at Nanjing Drum Tower Hospital. Plasma samples from these patients underwent proteomic analysis through the four-dimensional data-independent acquisition (4D-DIA) method, followed by bioinformatics analysis. Potential differentially expressed proteins (DEPs) were validated using enzyme-linked immunosorbent assay (ELISA). Sixty-six patients with knee OA were included and divided into responders (n=35) and non-responders (n=31). Proteomic analysis was conducted on 15 patients from each group, and ELISA validation was performed for every patient. We found 140 DEPs between the two groups after administering imrecoxib treatment, characterized by 29 proteins showing up-regulation and 111 displaying down-regulation (p < 0.05, fold change > ±1.2). Galectin-1 (LGALS1), galectin-3 (LGALS3), and the cluster of differentiation 44 (CD44) could be utilized to evaluate the clinical response to imrecoxib in the treatment of OA after ELISA validation.This study successfully identified biomarkers for evaluating imrecoxib's clinical response in OA patients using 4D-DIA technology. These biomarkers may play a vital role in future personalized OA treatment strategies, pending further confirmation.

2024-01-19 | PXD047236 | Pride

Characterization of the Angiogenic and Proteomic Features of Circulating Exosomes in a Canine Mandibular Model of Distraction Osteogenesis

Project description:While distraction osteogenesis (DO) can be an extremely effective approach to treating extensive bone defects, it entails a very long treatment period. The present study was designed with the goal of clarifying the mechanisms underlying the angiogenic and osteogenic activities characteristic of DO so as to identify promising therapeutic targets that may enable the enhancement of these activities in patients undergoing DO. Exosomes are key mediators of communication between cells, and they are thus well-positioned to influence DO-associated angiogenesis and osteogenesis. To explore their role in this context, a canine mandibular DO model was established, using a bone defect (BD) group as a control for experimental comparisons. Higher levels of angiogenesis were observed in the regenerating tissue from the DO group relative to the BD group, with these levels peaking in the early consolidation phase and being accompanied by earlier osteogenesis. Circulating exosomes were harvested during different phases of DO and subjected to proteomic characterization using a data-independent acquisition approach. These results revealed that the proteins present within these circulating exosomes reflect the regenerative activity observed in tissues undergoing DO, ultimately leading to the identification of FN1, THBS1, and TFRC as candidate proteins that may be related to the DO-related angiogenic activity. Subsequent cellular experiments confirmed the ability of DO-associated circulating exosomes to induce angiogenesis when used to treat endothelial cells. Together, these data reveal previously unknown mechanisms that may underlie the efficacy of DO, and suggest that exosome-derived proteins may offer utility as therapeutic targets for efforts aimed at enhancing DO-related angiogenesis and bone regeneration.

2025-05-13 | PXD050531 | Pride

Screening of candidate proteins affecting spermatogenesis by DIA analysis of testis proteomics in Shandong black cattle

Project description:All samples were processed by DIA individually to assess the proteome differences. MS1 and MS2 data were all acquired, and samples acquisition by random order. The iRT kit (Ki3002, Biognosys AG, Switzerland) was added to all of the samples to calibrate the retention time of extracted peptide peaks. The statistical analysis of the DIA dataset was performed by Spectronaut 16 (Biognosys AG, Switzerland) including data normalization and relative protein quantification.

2025-06-11 | PXD061007 | Pride

Antler stem cell-conditioned medium data independent acquisition

Project description:The process of chondrogenesis in deer antlers is very similar to that of mammalian cartilage formation. Antlers can regenerate at an alarming rate (up to 2 cm per day). To meet the rapid growth of antlers, paracrine factors play an important role. These paracrine factors promote the proliferation and growth of chondrocytes, regulate cartilage development and modulate cartilage phenotype. The application of stem cell paracrine factors for the treatment of cartilage defects avoids the problems of immunocompatibility, tumorigenicity, embolization, and infection. This study demonstrates that ASC-CM can effectively repair cartilage defects using in vitro and in vivo methods, providing a suitable cell source and pathway for cartilage repair and providing ideas for mechanisms to promote cartilage regeneration.

2023-04-11 | PXD041259 | Pride

DNAJA1 KO on HUVECs with heat stress

Project description:HS-induced proteome changes in WT and DNAJA1-KO cells were quantified using label free-based quantitative proteomic analysis. Four groups:wild type HUVECs group, DNAJA1 knockout HUVECs group, WT HUVECs with heat stress group, DNAJA1 knockout HUVECs with heat stress group,were conducted label free-based quantitative proteomic analysis to detect the mechanism of DNAJA1's protective effects on heat stress.

2024-03-26 | PXD043512 | Pride

Cx32 wt vs mutant purified proteins

Project description:An analysis of purified Cx32 wt, W3S and R22G mutations. The three different proteins were expressed, digested and measured in DIA.

2023-08-08 | PXD033848 | Pride

Integrated Fibre-Specific Methylome and Proteome Profiling of Human Skeletal Muscle Across Males and Females with Fibre-Type Deconvolution.

Project description:We simultaneously extracted DNA and protein from >200 single fibres per participant (7 males, 5 females) to directly compare methylome and proteome profiles of Type I and Type II human skeletal muscle fibres. Using the EPICv2 array and LC-MS/MS, we identified 5,689 robust DMRs (FDR <0.001) and 338 DEPs (FDR <0.001), revealing strong inverse correlations between methylation and protein abundance in key contractile and metabolic genes. We also built a TI/TII DNA methylation reference matrix and implemented fibre-type deconvolution (MyoTYPE) for whole-muscle samples, all accessible via the MyoMETH web resource.

2025-10-13 | PXD066393 | Pride