Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry (MS) datasets of QKI5 co-immunoprecipitation samples in THP-1 cells

ABSTRACT: We performed QKI5 co-immunoprecipitation followed by MS analysis to identify QKI5-interacting proteins in THP-1 cells.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yue Huo

LAB HEAD: Jia Yu

PROVIDER: PXD028743 | Pride | 2021-09-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	IgG-rep1-1.raw	Raw
	IgG-rep1-2.raw	Raw
	IgG-rep1-3.raw	Raw
	IgG-rep1.msf	Msf
	IgG-rep2-1.raw	Raw

Items per page:

1 - 5 of 16

Similar Datasets

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening 293T cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from 293T cells.

2021-09-27 | PXD028660 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening K562 cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from K562 cells.

2021-09-27 | PXD028668 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening THP-1 cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from THP-1 cells.

2021-09-27 | PXD028787 | Pride

HDAC8 regulates escape from BRAF inhibitor therapy in Melanoma: IMAC Phosphoproteomics

Project description:Melanoma cells are highly plastic and have the ability to switch to a dedifferentiated, invasive phenotype in response to multiple stimuli. Here, we show that exposure of melanoma cell lines and patient specimens to multiple stresses including BRAF-MEK inhibitor therapy, hypoxia and UV-irradiation leads to an increase in histone deacetylase 8 (HDAC8) expression/activity, and in turn, the adoption of a drug-resistant, invasive phenotype. Systems level analyses using mass spectrometry-based phosphoproteomics implicated HDAC8 in the regulation of MAPK and AP-1 signaling pathways. Introduction of HDAC8 into drug-naïve melanoma cells conveyed resistance both in vitro and in in vivo xenograft models. HDAC8-mediated BRAF inhibitor resistance was mediated via receptor tyrosine kinase (RTK) activation leading to Ras/CRAF/MEK/ERK signaling. Although HDACs primarily function at the histone level, they also regulate signaling through the modulation of non-histone substrates. In line with this, HDAC8 introduction decreased the acetylation of c-Jun, increasing its transcriptional activity and enriching for an AP-1 gene signature. Mutation of the putative c-Jun acetylation site at lysine residue 273 reduced the transcriptional activation of c-Jun in melanoma cells and conveyed resistance to BRAF inhibition through increased RTK expression and enhanced MAPK pathway activity. In vivo xenograft studies confirmed the key role of HDAC8 in therapeutic adaptation, with both non-selective and HDAC8-specific inhibitors enhancing the durability of response to BRAF inhibitor therapy. Our studies demonstrate that HDAC8-specific inhibitors could represent an excellent strategy to limit the adaptation of melanoma cells to multiple stresses and therapeutic interventions, including BRAF-MEK inhibitor combinations.

2020-07-07 | PXD012813 | Pride

Identification of proteins that interact with endogenous DHX9 from HeLa cell nuclear extracts

Project description:This project aims to identify proteins that interact with DHX9.

2024-06-12 | PXD044366 | Pride

Single-nucleus RNA-seq of the human musculotendinous unit, the myotendinous junction

Project description:Identification of cell types in the interphase between muscle and tendon by single-nuclei RNA-seq of three human semitendinous muscle-tendon biopsies. With special focus on the myotendinous junction specific myonuclei, transcripts were identified and confirmed to myotendinous junction with immunofluorescence.

2023-03-02 | E-MTAB-12529 | biostudies-arrayexpress

The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation

Project description:In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore. drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.

2020-07-21 | PXD018749 | Pride

Comparing the plasma membrane proteins of Nek1+/+ and Nek1Kat2J/Kat2J MEFs

Project description:Mass spectrometry data comparing the plasma membrane proteins of Nek1-WT and Nek1-Kat2J MEFs enriched by Pierce™ Cell Surface Protein Isolation Kit.

2021-08-06 | PXD027493 | Pride

Truncated PARP1 promotes RNA Polymerase III during apoptosis

Project description:The N-terminal three zinc finger motifs of PARP1 are evolutionarily conserved in multicellular organism。However, during apoptosis, human PARP1 is mainly cleaved by caspase 3 at D214. As a result, the truncated PARP1 loses two N-terminal zinc finger motifs and only contains the third zinc finger motif, the BRCT domain, the WGR domain and the C-terminal catalytic domain. Interestingly, when we explored the domain architecture of PARP1 in other organisms, we found that similar to human tPARP1, PARP1 orthologs in several lower organisms do not have the N-terminal two zinc fingers or even they lack the third zinc finger motif. It indicates that even without the first two zinc finger motifs, tPARP1 may still catalyze ADP-ribosylation and play an important role in certain biological processes. To reveal the biological function of tPARP1, we performed tandem affinity purification and searched for the possible substrates.

2022-02-15 | PXD018691 | Pride

USP8 maintains ESC stemness via deubiquitination of EPG5

Project description:The coiled-coil domain of EPG5 was synthesized as follows: Biotin-MNKNEAVSQQIHVLQKEVRQLQAE AAQ (from Beijing SciLight Biotechnology, LCC). 1 mg of this short peptide was incubated with ES cells lysates followed by immunoprecipitation with anti-biotin beads. The precipitates were extensively washed with lysis buffer then boiled with SDS loading buffer and subjected to SDS–PAGE. Total proteins were excised from the gels, then subjected to in-gel digestion and analysis by LC-MS/MS.

2019-02-25 | PXD012563 | 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