Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tomato SlLYK13 Phosphorylation LC-MS/MS

ABSTRACT: To identified the key phosphorylation residues of SlLYK13 in vitro, we performed liquid chromatography–tandem mass spectrometry (LC-MS/ MS) of the MBP-SlLYK13CD and GST-SlLYK4CD or GST-EV (mock) after in vitro kinase assays.

ORGANISM(S): Solanum Lycopersicum

SUBMITTER: Bo Li

PROVIDER: PXD076007 | iProX | Mon Mar 23 00:00:00 GMT 2026

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Tomato SlLYK4 Phosphorylation LC-MS/MS

Project description:To identify the key phosphorylation residues of SlLYK4, we performed liquid chromatography-tandem mass spectrometry (LC-MS/MS)in vitro kinase assays with liquid of GST-SlLYK4 and MBP-SlLYK13CD or MBP (mock) after in vitro kinase assays. And then SlLYK4-FLAG was transiently expressed in tomato hairy roots and samples were collected post EPS or chitin treatment, followed by immunoprecipitation-mass spectrometry analysis.

2024-08-29 | PXD055434 |

Phosphorylation site identifcaiton of OsHSFA4d

Project description:To identify the residues of OsHSFA4d phosphorylated by OsCDPK24, the in vitro kinase assays were conducted by incubating recombinant MBP-HA-OsCDPK24 + GST-OsHSFA4d and MBP-HA + GST-OsHSFA4d. The reaction was terminated by adding SDS loading buffer to a 1×concentration, and the reaction products were subjected to CBB staining and immunoblot analysis as described above. The CBB-stained protein bands corresponding to phosphorylated OsHSFA4d were excised and subjected to LC-MS/MS analysis.

2025-06-09 | PXD064745 | Pride

Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock

Project description:The importance of oligogalacturonides for plant defence and growth has been described extensively in litterature. However, much of previous global transcriptome analyses for plants treated with oligogalacturonides have focused on long (>10 galacturonosyl residues) oligogalacturonides. This study focuses on the transcriptomic impact that short (<10 galacturonosyl residues) oligogalacturonides have on plant transcriptomes and overall biology. Arabidopsis seedling were grown on liquid 1/2 MS medium in 12-well culture plates in vitro for 12 days. 12 seedlings were cultured per well, and three wells were combined per biological replicate. The seedling plants were treated either with 1/2 MS medium (mock), 1/2 MS with trimeric oligogalacturonides (trimers) and a mixture of 1/2 MS and oligogalacturonides (short OG-mix) containing 2-9 residues for 3 hours. RNA was extracted from the seedlings, three biological replicates per treatment, and sequenced using the SOLiD 5500XL platform.

2015-06-05 | E-GEOD-69538 | biostudies-arrayexpress

Extracellular vesicles-derived miR-760 and miR-98-5p as differentiating biomarkers for MS phenotypes

Project description:Objective. Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system with heterogenous clinical course, lacking non-invasive biomarkers for early phenotype differentiation. This study aimed to identi-fy circulating extracellular vesicle (EV)-derived miRNA signatures and as-sociated disease-specific molecular markers capable of distinguishing stable relapsing-remitting MS (RRMS) from secondary progressive MS (SPMS). Materials and methods. Plasma samples were collected from patients with stable RRMS, SPMS, and healthy controls (HC), followed by EVs isolation and characterization using transmission electron microscopy, dynamic light scattering, and flow cytometry. RNA was extracted from EVs, and miRNA profiles were ana-lyzed via RNA sequencing and RT-qPCR. Cytokine and neurodegeneration marker levels were quantified using the BioPlex® multiplex system and ELISA. Functional enrichment and network analyses of miRNA targets were performed, alongside logistic regression modeling to assess diagnostic utility. Results. Four EV-derived miRNAs (miR-760, miR-98-5p, miR-301a-3p, and miR-223-3p) showed significant differences between stable RRMS and SPMS. The integrative model incorporating these miRNAs with FGF basic protein achieved excellent discrimination between MS phenotypes (AUC = 0.97). Moreover, miR-760 emerged as the most robust predictive biomarker for stable RRMS classification. In turn, miR-98-5p showed the highest up-regulation in both stable RRMS and SPMS relative to HC. miRNA targets network analysis further revealed distinct immunoregulatory patterns for stable RRMS and SPMS. Conclusions. Plasma-derived EV-miRNAs, particularly miR-760 and miR-98-5p, showed strong potential as non-invasive biomarkers for stable RRMS and SPMS phenotypes. Integrating EV-miRNA profiling with protein bi-omarkers enhances diagnostic precision and may support personalized management strategies in MS.

2026-02-11 | GSE303912 | GEO

Glomus sp. MS strain:MS

Project description:Glomus sp. MS strain:MS Genome sequencing

| PRJNA210520 | ENA

Methanosarcina barkeri MS strain:MS

Project description:Methanosarcina barkeri MS strain:MS Raw sequence reads

| PRJNA613292 | ENA

CPK3 enhances CNGC activity by phosphorylation of CNGC6 phos site

Project description:LC-MS/MS and in vitro phosphorylation assays, CPK3, CNGC6-N, and CNGC6-C, and point-mutated CNGC6-N-C were cloned into the vector pGEX4T-1 downstream of the GST tag, and the recombinants were expressed in and purified from E. coli BL21-Gold (DE3)

2025-07-29 | PXD066699 |

A phosphorylation-dependent ubiquitination switch orchestrates nuclear immune reprogramming upon chitin perception

Project description:OsRLCK185 is a functional kinase, we then examined whether OsRLCK185 phosphorylates OsPUB20 using an in vitro kinase assay, OsRLCK185K108A served as a negative control. The results showed that GST-OsRLCK185, but not GST-OsRLCK185K108A, phosphorylates OsPUB20 in vitro. Using LC-MS/MS analysis after an in vitro phosphorylation reaction with GST-OsRLCK185 and His-OsPUB20, we identified threonine 153 (T153), located between U-box domain and ARM repeats of OsPUB20, as the OsRLCK185 phosphorylation site.

2026-01-29 | PXD073757 |

siRNA-mediated knockdown of Sp3 induces a pro-inflammatory pattern of cytokine production: relevance to MS

Project description:Multiple sclerosis (MS) is an inflammatory disease of the central nervous system and is generally considered to be autoimmune in nature. We previously demonstrated that the transcription factor Sp3 is significantly down-regulated in immune cells from MS patients. The potential role of Sp3 down-regulation in MS pathogenesis is not well understood. The function of endogenous Sp3 was assessed in vitro after siRNA-mediated knockdown of its transcript in Jurkat cells. Sp3 protein levels were reduced an average of 70%. ELISA studies demonstrated decreased endogenous production of IL-10 and TGFβ1 and increased endogenous production of TNFα (p<0.05 in all assays). Subsequent microarray analysis demonstrated significantly altered expression of 36 genes (p<0.001 for each gene) compared with control samples. Analysis showed differential expression (p<0.005) of 8 gene pathways. Many of the genes and pathways that were regulated by Sp3 are involved in immune function, specifically with regard to apoptosis, cell-to-cell adhesion, integrin signaling, T-cell differentiation, and cytokine production. This study identifies mechanisms by which Sp3 may regulate immune function and suggests a basis for its potential contribution to MS disease pathogenesis. Keywords: siRNA knockdown; Jurkat T-cells; Multiple Sclerosis

2008-02-21 | GSE7102 | GEO

Project description:We found that LC3B is phosphorylated in vitro by STK3, STK4, NEK9, and PKCζ. To identify phosphorylation sites following in vitro phosphorylation, GST-LC3B was overexpressed in E. coli, purified using glutathione-Sepharose 4 Fast Flow beads and incubated in kinase assays with recombinant kinases or FLAG-tagged kinases immunopurified from transiently transfected HEK293 cells

2020-01-23 | PXD016681 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data