Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of proteins interacting with the NEK1-C21ORF2 complex

ABSTRACT: We and others have found that the NEK1 kinase interacts with the C21ORF2 protein. Gel filtration indicated there may be other proteins in the complex. We tried to identify such proteins by immunoprecipitating endogenous NEK1 from cells and subjecting the precipitates to mass spectrometry. We also immunoprecipitated endogenous NEK1 from cells and subjected the precipitates to mass spectrometry. To find the full complement of NEK1 interactors, NEK1 was immunoprecipitated from ARPE-19 parental cells, and NEK1-KO cells were to control for non-specific binding. Five biological replicates were used per cell line, and after trypsinization of the precipitates, peptides were labelled with tandem mass tags (TMT) enabling quantitative mass spectrometric analysis of the 10 samples which were pooled and analysed in parallel. To find the full complement of C21ORF2 interactors, C21ORF2 was immunoprecipitated from ARPE-19 parental cells, and C21ORF2-KO cells were to control for non-specific binding. Five biological replicates were used per cell line, and after trypsinization of the precipitates, peptides were labelled with tandem mass tags (TMT) enabling quantitative mass spectrometric analysis of the 10 samples which were pooled and analysed in parallel.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Frederic Lamoliatte

LAB HEAD: John Rouse

PROVIDER: PXD036410 | Pride | 2023-05-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20211208_FL_Mat_JR_CB_Fraction01.raw	Raw
	20211208_FL_Mat_JR_CB_Fraction02.raw	Raw
	20211208_FL_Mat_JR_CB_Fraction03.raw	Raw
	20211208_FL_Mat_JR_CB_Fraction04.raw	Raw
	20211208_FL_Mat_JR_CB_Fraction05.raw	Raw

Items per page:

1 - 5 of 25

Similar Datasets

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

Entamoeba histolytica splicing/mRNP proteome

Project description:First, the snRNP component U1A was HA-tagged and the intron of the RabX13 gene was MS2-tagged and amoeba transformats were established with such constructs. Next, amoeba transformants were UV cross-linked and their nucler extracts were immunoprecipitated (IP) with anti-HA agarose or MS2-spharose beads. Precipitates were subjected to tandem mass spectrometry (MS/MS) analyses. MS2-IP helped to discriminate the nuclear roles (chromatin-, co-transcriptional-, splicing-related), of the proteins probed.

2014-09-11 | PXD001080 | Pride

Gene expression signitures in ARPE-19 cells treated with or without TGF-β1

Project description:To identify the dysregulated lncRNA and mRNA expression in ARPE-19 cells underwent EMT, we established a TGF-β1 induced EMT model of ARPE-19 cells. ARPE-19 cells were treated with or without 10 ng/ml TGF-β1 for 48 h. Total RNA are extracted and subjected to microarray assay (Arraystar Human LncRNA Microarray V3.0)

2021-08-11 | GSE105053 | GEO

Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

Project description:DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized, however the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by EdU-labelling for Mass Spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows hydroxymethylation is perpetually asymmetric between sister strands in favor of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation-histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.

2022-10-24 | GSE193681 | GEO

Host response profile of human brain proteome in toxoplasma encephalitis

Project description:Frontal cortex brain tissues obtained from 5 toxoplasma encephalitis patients and 5 controls were used for protein extraction. Protein amount was normalized on 10% SDS-PAGE, equal amount of protein from 5 patients and 5 controls were pooled separately and subjected to reduction, alkylation and trypsin digestion. iTRAQ labelling of samples were carried out in replicates. Peptides from control samples were labelled with iTRAQ labels leading to the reporter ions of 114 and 115 whereas peptides from patient samples were labelled with iTRAQ labels leading to the reporter ions of 116 and 117. Labelled peptides were then pooled and subjected to SCX fractionation and obtained 21 fractions, which were subsequently subjected to high-resolution Fourier transform mass spectrometry (LTQ-Orbitrap Velos).

2016-05-09 | PXD000261 | Pride

Arraystar m6A-mRNA&lncRNA Epitranscriptomic Microarray Service for 6 Mouse samples

Project description:Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, the total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol. The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar). After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

2022-11-24 | GSE218412 | GEO

ARPE-19_adriamycin_gene_expression

Project description:This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment ARPE-19 cells were treated with 1Î¼M adriamycin for 24 h compared with control

2016-03-01 | E-GEOD-78765 | biostudies-arrayexpress

GNPS - 20-37 kDa band of HSPA1A IP (Table S3, Prophet et al.)

Project description:HSPA1A was immunoprecipitated from WT or TorsinKO HeLa cells. A band around 27 kDa was uniquely found to co-immunoprecipitate with HSPA1A in TorsinKO cells. To identify this band, it was extracted and subjected to mass spectrometry.

2022-08-23 | MSV000090187 | GNPS

Stretch growth does not alter gene expression

Project description:Differentiated PC12 cells were magnetically labeled with magnetic nanoparticles (MNP). External magnetic fields were used to mechanically stretch the MNP-labeled neurites. We found that mechanical stretching of the neurites induces mass addition and neurite elongation. We performed RNAseq of MNP-labelled cells in stretched versus non-stretched conditions and we did not found gene expression dysregulation, confirming that the two conditions were identical and excluding cytotoxicity or involvement of nuclear mechanotransdution. Indeed, local mechanisms triggered by the stretching of the MNP-labelled neurite would be responsible for neurite elongation.

2018-06-08 | GSE115474 | GEO

Expression Data from DMSO or SRPIN803 treated ARPE-19 cells

Project description:We used microarrays to evaluate the effect of SRPIN803 on gene expression in ARPE-19 cells. ARPE-19 cells were treated with SRPIN803 (10 uM) or the negative control (0.1% DMSO) for 4 hours for Total RNA isolation and hybridization on Microarray.

2015-06-17 | E-GEOD-62947 | biostudies-arrayexpress

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