Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Zebrafish caudal fin phosphoproteomic of Rps6kb1a/b knockdown

ABSTRACT: Knocked-down of P70S6K in zebrafish (double knockdown of rps6kb1/2) using embryo Cas9/gRNA RNP injections followed by phosphoproteomics of caudal fin.

INSTRUMENT(S):

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Tail

SUBMITTER: Benjamin Parker

LAB HEAD: Benjamin Parker

PROVIDER: PXD054212 | Pride | 2025-12-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	220822_Exploris_BenParker_BP-4737_A1.raw	Raw
	220822_Exploris_BenParker_BP-4737_A2.raw	Raw
	220822_Exploris_BenParker_BP-4737_B1.raw	Raw
	220822_Exploris_BenParker_BP-4737_B2.raw	Raw
	220822_Exploris_BenParker_BP-4737_C1.raw	Raw

Items per page:

1 - 5 of 31

Similar Datasets

Proteomic analysis of NFIX over-expression in C2C12 myotubes

Project description:Overexpressed either GFP, wild-type (WT) NFIX or a phospho-dead mutant of NFIX in which eight serine residues surrounding S286 were mutated to alanine (S265/267/268/271/272/273/274/275A) was performed C2C12 cells prior to the induction of myogenesis. Cells were harvest 2 days post induction of myogensis with 2% horse serum.

2022-05-18 | PXD028718 | Pride

Identification of K12 binding partners

Project description:The compound K12 has been identified as a novel inhibitor of the oncogenic functions of the JNK pathway through a phenotypic drug screen. This analysis has been performed to identify the direct protein target/s of K12.

2025-04-05 | PXD061936 | Pride

Merlin S13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features

Project description:Meningiomas are the most common primary intracranial tumors and are associated with inactivation of the tumor suppressor NF2/Merlin, but one-third of meningiomas retain Merlin expression and typically have favorable clinical outcomes. Biochemical mechanisms underlying Merlin-intact meningioma growth are incompletely understood, and non-invasive biomarkers that predict meningioma outcomes and could be used to guide treatment de-escalation or imaging surveillance of Merlin-intact meningiomas are lacking. Here we integrate single-cell RNA sequencing, proximity-labeling proteomic mass spectrometry, mechanistic and functional approaches, and magnetic resonance imaging (MRI) across meningioma cells, xenografts, and human patients to define biochemical mechanisms and an imaging biomarker that distinguish Merlin-intact meningiomas with favorable clinical outcomes from meningiomas with unfavorable clinical outcomes. We find Merlin drives meningioma Wnt signaling and tumor growth through a feed-forward mechanism that requires Merlin dephosphorylation on serine 13 (S13) to attenuate inhibitory interactions with β-catenin and activate the Wnt pathway. Meningioma MRI analyses of xenografts and human patients show Merlin-intact meningiomas with S13 phosphorylation and favorable clinical outcomes are associated with high apparent diffusion coefficient (ADC) on diffusionweighted imaging. In sum, our results shed light on Merlin posttranslational modifications that regulate meningioma Wnt signaling and tumor growth in tumors without NF2/Merlin inactivation. To translate these findings to clinical practice, we establish a non-invasive imaging biomarker that could be used to guide treatment de-escalation or imaging surveillance for patients with favorable meningiomas.

2024-07-04 | PXD053578 | Pride

Proteomic analysis of single muscle fibres from WT and C18ORF25 KO mice

Project description:C18ORF25 is a homolog of Arkadia (RNF111), an E3 ubiquitin ligase with SUMO-interaction motifs (SIMs) (PMID: 31417085). However, C18ORF25 lacks the entire C-terminal RING domain of RNF111 which is required for ubiquitin binding suggesting it lacks ubiquitination activity and may therefore act as an adaptor or signalling scaffold (PMID: 26283374). We have previously shown that mice lacking C18Orf25 throughout the entire body have increased adiposity, decreased lean mass, lower exercise capacity and significantly reduced ex vivo skeletal muscle force production (PMID: 35882232). Skeletal muscle isolated from C18Orf25 knockout (KO) mice have reduced cAMP-dependent protein kinase A (PKA) levels, and reduced phosphorylation of several contractile proteins and proteins involved in calcium handling. Furthermore, analysis of single muscle fibres from C18Orf25 KO mice revealed impaired SR calcium cycling in fast-twitch fibres only (PMID: 35882232). Hence, we investigated these mechanisms by developing an integrated single-fibre physiology and single-fibre proteomic platform. The platform enabled us to identify hundreds of novel phenotype:protein correlations. The analysis also enabled us to identify proteome differences specifically in FT fibres following loss of C18ORF25. Taken together, our data suggest C18ORF25 is likely a multi-functional protein with several underlying mechanisms contributing to skeletal muscle physiology.

2024-01-03 | PXD045631 | Pride

Proteomic and secretomic analysis of Kusa 4B10 osteoblasts

Project description:Kusa 4B10 mesenchymal stem cells (MSCs) were differentiated into osteoblasts over 21 days and either left untreated as controls or made insulin resistant via hyperinsulinemia treatment over 2 days prior to a proteomic and secretomic analysis.

2025-12-16 | PXD054479 | Pride

Proteomic and phosphoproteomic of C2C12 myogenesis and MAPK inhibition

Project description:Myogenesis is governed by signalling networks whose regulations are tightly controlled in a time-dependent manner. While different protein kinases have been identified to regulate various aspects of myogenesis, knowledge on the global signalling networks and their downstream substrates during myogenesis remains incomplete. Here, we map the myogenic differentiation of C2C12 cells using mass spectrometry (MS)-based phosphoproteomics and proteomics. From these data, we infer global kinase activity and predict substrates of key kinases that are involved in myogenesis. We found that multiple mitogen-activated protein kinases (MAPKs) mark the initial wave of signalling cascades. Further phosphoproteomic and proteomic profiling with MAPK1/3 and MAPK8/9 specific inhibitions unveil their shared and distinctive roles on myogenesis.

2022-05-31 | PXD028713 | Pride

Interactome analysis of ACAD11 in HEK293 cells

Project description:Affinity purification - mass spectrometry analysis of N-terminally FLAG-tagged ACAD11 transietly expressed in HEK293 cells.

2019-03-14 | PXD010788 | Pride

A family of unconventional deubiquitinases with modular chain specificity determinants

Project description:Interactors of human ZUFSP in HEK-293T cells. Flp-in T-REx 293 cells with stable 3xFLAG-ZUFSP integration were assayed for ZUFSP interactors under three different conditions: i) Cells expressing wild-type ZUFSP, ii) Cells expressing catalytically inactive ZUFSP, iii) Cells expressing wild-type ZUFSP with additional treatment by an unspecific nuclease (Benzonase) during purification.

2018-04-06 | PXD008731 | Pride

Proteomic analysis of L6 myoblasts treated with C-terminal transgelin peptides

Project description:To investigate bioactivity of peptides identified in human plasma, we treated L6 myoblasts in vitro with a synthetic C-terminal peptide from TAGLN spanning amino acids 179-200, or a synthetic C-terminal peptide from TAGLN2 spanning amino acids 178-199 (1 µg/mL; 7 days), and compared the treatments to control myoblasts cultured for the same amount of time with the addition of only PBS. Proteomic analysis by single-shot nanoUHPLC-MS/MS was performed on four biological replicates and quantification performed by LFQ. A total of 6,095 proteins were identified with 4,710 quantified in at least three biological replicates (Supplemental Table S4). A total of 222 and 307 proteins were regulated by the TAGLN and TAGLN2 peptides relative to the control treatments, respectively, with 61 proteins co-regulated by both TAGLN and TAGLN2 (P<0.05; two-sample t-test with Benjamini-Hochberg correction) (Figure 3G).

2017-11-21 | PXD007176 | Pride

Affinity purification – mass spectrometry of AFF4 WT or S829/S831/3/5/8A mutant

Project description:The S831 phosphosite on AFF4 lies within a disordered region adjacent to the ENL/AF9 binding site. We therefore hypothesized that phosphorylation may regulate protein:protein interactions within the Super Elongation Complex. To investigate this, HEK293T cells expressing RFP negative control, FLAG-tagged AFF4-WT or FLAG-tagged AFF4-A-mutant were stimulated with insulin for 30 min followed by immunoprecipitation and analysis of interacting proteins by LC-MS/MS.

2025-12-16 | PXD054250 | 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