Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PPP6R3 immunoprecipitation mass spectrometry (IP-MS) data

ABSTRACT: PPP6R3 IP-MS data using KIT+ spermatogonia purified from testes of P9 wild-type mice

ORGANISM(S): Mus Musculus

SUBMITTER: Hongbin Liu

PROVIDER: PXD056272 | iProX | Wed Sep 25 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

PPP6R3-mediated dephosphorylation regulates mRNA translation during spermatogonial differentiation.

Fang Qian Q Liu Biyun B Cen Jie J Li Tongtong T Ji Shuhui S Li Wenqing W Lu Gang G Chen Zi-Jiang ZJ Wang Xin X Bao Jianqiang J Liu Hongbin H

Communications biology 20250728 1

Protein dephosphorylation mediated by phosphatases regulates spermatogenesis. However, which proteins are dephosphorylated and how they regulate spermatogenesis are largely unknown. Here, we show that germline-specific deletion of protein phosphatase 6 regulatory subunit 3 (PPP6R3), which determines substrate specificity of protein phosphatase 6 (PP6), causes abnormal spermatogonial differentiation and male infertility, accompanied by translation inhibition. PPP6R3 directly interacts with EIF3C ...[more]

PMID: 40721635

Similar Datasets

Detection of a rare BCR-ABL tyrosine kinase fusion protein in H929 multiple myeloma cells using immunoprecipitation (IP)-tandem mass spectrometry (MS/MS).

Project description:Hypothesis directed proteomics offers higher throughput over global analyses. We show that immunoprecipitation (IP)-tandem mass spectrometry (LC-MS/MS) in H929 multiple myeloma (MM) cancer cells led to the discovery of a rare and unexpected BCR-ABL fusion, informing a therapeutic intervention using imatinib (Gleevec). BCR-ABL is the driving mutation in chronic myeloid leukemia (CML) and is uncommon to other cancers. Three different IP-MS experiments central to cell signaling pathways were sufficient to discover a BCR-ABL fusion in H929 cells: phosphotyrosine (pY) peptide IP, p85 regulatory subunit of phosphoinositide-3-kinase (PI3K) IP, and the GRB2 adaptor IP. The pY peptides inform tyrosine kinase activity, p85 IP informs the activating adaptors and receptor tyrosine kinases (RTKs) involved in AKT activation and GRB2 IP identifies RTKs and adaptors leading to ERK activation. Integration of the bait-prey data from the three separate experiments identified the BCR-ABL protein complex, which was confirmed by biochemistry, cytogenetic methods, and DNA sequencing revealed the e14a2 fusion transcript. The tyrosine phosphatase SHP2 and the GAB2 adaptor protein, important for MAPK signaling, were common to all three IP-MS experiments. The comparative treatment of tyrosine kinase inhibitor (TKI) drugs revealed only imatinib, the standard of care in CML, was inhibitory to BCR-ABL leading to down-regulation of pERK and pS6K and inhibiting cell proliferation. These data suggest a model for directed proteomics from patient tumor samples for selecting the appropriate TKI drug(s) based on IP and LC-MS/MS. The data also suggest that MM patients, in addition to CML patients, may benefit from BCR-ABL diagnostic screening.

| S-EPMC3479604 | biostudies-literature

immunoprecipitation-mass spectrometry (IP-MS) of FDR-1

Project description:immunoprecipitation-mass spectrometry (IP-MS)of FDR-1

2025-08-07 | PXD066847 | Pride

Mouse adult testes: Total RNA vs. IP RNA

Project description:RNAs that are enriched in AGO2 Immunoprecipitated (IP) products or PIWIL1 IP products were identified from mouse(BALB/C) adult testes by examine the ratio of total RNA signal intensity to AGO2 IP RNA or PIWIL1 IP RNA signal intensity. Two-condition experiment,Total RNA extracted from mouse adult testes vs. AGO2 IP RNA extracted from mouse adult testes and total RNA extracted from mouse adult testes vs. PIWIL1 IP RNA extracted from mouse adult testes.

2013-04-01 | E-GEOD-27582 | biostudies-arrayexpress

Co-immunoprecipitation followed by mass spectrometry (Co-IP/MS) data of HNRNPF.

Project description:The interacting proteins of HNRNPF were identified in mouse embryonic stem cells by co-immunoprecipitation followed by mass spectrometry (Co-IP/MS).

2025-06-30 | PXD065613 | Pride

Discovery of Klf2 Interactors in Mouse Embryonic Stem Cells by Immunoprecipitation-Mass Spectrometry Utilizing Exogenously Expressed Bait

Project description:We report the RNA-seq data of Klf2 knockdowned cells and Snd1 knockdowned cells from mouse embryonic stem cells. Samples were lysed with total RNA prep kit.

2021-03-24 | GSE169406 | GEO

Immunoprecipitation and mass spectrometry (IP-MS) on KAT6A chimeras

Project description:Despite KAT6A chimeras potent oncogenic activity, the mechanisms by which KAT6A fusion proteins achieve genomic specificity and drive leukemogenesis remain poorly understood. Previous studies suggest that the leukemogenic potential of KAT6A-TIF2 depends on its chromatin-binding ability rather than its histone acetyltransferase (HAT) activity, with oncogenicity further amplified by CBP recruitment through its fusion partners. The winged helix domain (WH1) of KAT6A can bind unmethylated CpG islands and interact with P300/CBP via the TAZ2 domain. However, the widespread presence of unmethylated CpG islands across the genome does not fully explain the genomic specificity of KAT6A-CBP (K/C) and KAT6A-P300 (K/P) fusions, leaving key mechanistic gaps unexplored. To uncover protein interactions underlying these genomic associations, we performed immunoprecipitation and mass spectrometry (IP-MS) on KAT6A N-terminus and chimeras. Mass spectrometry analysis was performed to identify the core components of the KAT6A complex and the interacting proteins of KAT6A.

2025-08-08 | PXD061491 | Pride

Mouse adult testes: Total RNA vs. IP RNA

2013-04-01 | GSE27582 | GEO

Identification of antigenic proteins from the venom of Malaysian snakes using immunoprecipitation assay and tandem mass spectrometry (LC-MS/MS).

Project description:Snake envenomation poses a significant risk to Malaysians and country visitors. Malaysia witnesses an estimated 650 snake bites per 100,000 population annually. The primary treatment for snake envenomation involves administering antivenom derived from horses, despite its drawbacks, such as anaphylactic reactions and serum sickness. Identifying the venom proteome is crucial for understanding and predicting the clinical implications of envenomation and developing effective treatments targeting specific venom proteins. In this study, we employ an immunoprecipitation assay followed by LC-MS/MS to identify antigenic proteins in five common venomous snakes in Malaysia compassing of two families which are pit vipers, (Calloselasma rhodostoma and Cryptelytrops purpureomaculatus) and cobras (Ophiophagus hannah, Naja kaouthia, and Naja sumatrana). The immunoprecipitation assay utilises a 2 % agarose gel, allowing antigenic proteins to diffuse and bind with antibodies in the antivenom. The antivenom utilised in this research was procured from the Queen Saovabha Memorial Institute (QSMI), Thailand, including king cobra antivenom (KCAV), cobra antivenom (CAV), Malayan pit viper antivenom (MPAV), Russell's viper antivenom (RPAV), hematopolyvalent antivenom (HPAV), neuropolyvalent antivenom (NPAV), banded krait antivenom (BKAV), and Malayan krait antivenom (MKAV). The protein identified through these interactions which are exclusive to the cobras are three-finger toxins (3FTXs) while snake C-type lectins (Snaclecs) are unique to the pit vipers. Common protein that are present in both families are L-amino acid oxidase (LAAO), Phospholipase A2 (PLA2), and snake venom metalloproteinase (SVMP). Identifying these proteins is vital for formulating a broad-spectrum antivenom applicable across multiple species.

| S-EPMC11403504 | biostudies-literature

Mili-IP, Miwi-IP, and total RNA from mouse adult testis

Project description:We deep-sequenced small RNAs after immunoprecipitation of Mili or Miwi, as well as total small RNA from adult mouse testis. The goal of this experiment is to more deeply characterize the piRNA pool from adult mouse testes, using the Illumina platform. Comparison of 2 IP libraries with a non-IP library

2010-01-04 | E-GEOD-19172 | biostudies-arrayexpress

Immunoprecipitation (IP)-mass spectrometry analysisin of REIIBP in Hela cells

Project description:To investigate the functions of REIIBP, we conducted the immunoprecipitation (IP)-mass spectrometry analysis to identify the interacting proteins of REIIBP.

2025-10-06 | PXD062854 | 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