Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

293T NME4 TAP-MS and TurboID-MS

ABSTRACT: To identify interacting proteins of NME4 in human cell lines, we using tandem affinity purification followed by mass spectrometry (TAP-MS) in HEK293T cells. We established stable cell line which expressing NME4 gene fused with SFB triple tags (S tag-2x Flag tag-SBP tag) or TurboID. We isolated, combined, and affinity-purified the membrane and soluble fractions using TAP. We identified proteins associated with the bait in the isolated complexes using MS and searched the uniprot human database for these proteins.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Fibroblast, Kidney

SUBMITTER: shaofang xie

LAB HEAD: Xu Li

PROVIDER: PXD036624 | Pride | 2023-10-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	NME4-1.msf	Msf
	NME4-1.raw	Raw
	NME4-2.msf	Msf
	NME4-2.raw	Raw
	NME4-T1.msf	Msf

Items per page:

1 - 5 of 9

Similar Datasets

Enrichment of NICD4 interacting proteins by three different methods.

Project description:There are several methods to bring down the bait and interactors from the cell lysates, each with its own advantages and disadvantages. Recently, the most commonly used method is one step AP, TAP and proximity-labeling. In order to analyze the Strengths and weaknesses of the three methods, fusion proteins were constructed by NICD4 with FLAG, SFB (S tag-2x Flag tag-SBP tag) and TurboID respectively, NICD4 and its interactors were obtained by purification. By analyzing these proteins, we believe that SFB-TAP is the most reliable and effective method to identify interacting proteins.

2022-08-12 | PXD031772 | Pride

FBL promotes cancer cell resistance to DNA damage by transcriptionally regulating BRCA1 via YBX1

Project description:In order to study the molecular mechanism of FBL in cells, this project constructed the full length of FBL into the SFB (S-Flag-SBP tag) vector, and constructed a stable cell line overexpressing FBL. Affinity chromatography combined with LC-MS/MS technology to screen FBL interacting proteins.

2023-07-26 | PXD034434 | Pride

SFB-tagged(S-protein tag, Flag epitope tag, and streptavidin-binding peptide tag) RNF4 wild-type and CS mutant LC-MSMS

Project description:To elucidate the role of RNF4 in DNA replication and fork reversal, we performed tandem affinity purification (TAP) using a HEK293T cell line that stably expresses SFB-tagged(S-protein tag, Flag epitope tag, and streptavidin-binding peptide tag) wild-type and CS mutant to isolate proteins that associate with RNF4.

2022-08-11 | PXD028397 | Pride

Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals

2012-03-01 | GSE32941 | GEO

Features of TAP independently presented MHC ligands revealed by quantitative mass spectrometry.

Project description:The TAP transporter is responsible for transferring cytosolic peptides into the ER where they can be loaded onto MHC molecules. Deletion of TAP results in a drastic reduction of MHC surface expression and alters the presented peptide pattern. Using the TAP deficient cell line LCL721.174 and its TAP expressing progenitor cell line LCL721.45, we have identified and quantified more than 160 HLA ligands, 50 out of which were presented TAP independently. Peptides which were predominantly presented on the TAP deficient LCL721.174 cell line had a decreased MHC binding affinity according to their SYFPEITHI and BIMAS score. About half of the identified TAP independently presented peptides were not derived from signal sequences and may partly be generated by the proteasome. Furthermore, we have excluded that different HLA presentation ratios were due to varying expression of the respective protein or due to changes in the antigen loading complex. Features of TAP-independently presented peptides as well as proteasomal contribution to their generation provides an insight into basic immunological mechanisms. Keywords: differential mass spectrometry, TAP independent, antigen presentation

2007-10-27 | GSE9437 | GEO

CLIP-seq of S. cerevisiae Drn1-TAP and Dbr1-TAP

Project description:Data for replicate Drn1-TAP and Dbr1-TAP CLIP-seq experiments to identify RNA-protein interactions

2013-06-28 | GSE44959 | GEO

Expression profile of TAP tagged Tho2 strain

Project description:Tho2 protein was tagged with a TAP tag and the gene expression profile was compared to an untagged wildtype strain of the same background using DNA microarrays

2013-09-24 | E-MTAB-1892 | biostudies-arrayexpress

Three acyltransferases and a nitrogen responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas

Project description:Three acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumulation based on their patterns of expression. Each gene also shows increased mRNA abundance in other TAG-accumulating conditions (-S, -P, -Zn, -Fe). Insertional mutants, pdat1-1 and pdat1-2, accumulate 25% less TAG compared to the parent strain, D66+, which demonstrates the relevance of the trans-acylation pathway in Chlamydomonas. The biochemical functions of DGTT1 and PDAT1 were validated by rescue of oleic acid sensitivity and restoration of TAG accumulation in a yeast strain lacking all acyltransferase activity. Time course analysis suggest than an SBP domain transcription factor protein, whose mRNA increases precede that of other genes like DGAT1, is a candidate regulator of the N-deficiency response. An insertional mutant, nrr1-1, accumulates only 50% of the TAG compared to the parental strain in N-starvation conditions and is unaffected by other nutrient stresses, suggesting the operation of multiple signaling pathways leading to stress-induced TAG accumulation. Sampling of Chlamydomonas 2137 cultivated in TAP, N-Free TAP or TAP with varying amounts of N.

2013-01-10 | E-GEOD-34585 | biostudies-arrayexpress

LC-MS/MS Proteomics analysis of PDL1 protein in 293T cell line

Project description:To identify the proteins interact with PDL1 protein in human cell lines, we analyzed the protein complexes using tandem affinity purification followed by mass spectrometry (TAP-MS) in HEK293T. We established the cell lines stably expressing PDL1 gene fused with Flag tags. We identified proteins associated with the bait in the isolated complexes using MS and searched the human databases for these proteins.

2022-10-13 | PXD031702 | Pride

Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals

Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein We purified TAP::ALG-1 complexes from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2, serving as a mock control) animals and hybridized the associated mRNAs to two-color microarrays RNA isolated from WS4303 and N2 (mock control) animals was analyzed for each IP sample and for each total worm extract sample. Three independent biological replicates have been performed. Long-oligo whole-genome C. elegans arrays, produced by the Genome Sequencing Center at Washington University in St. Louis (http://genome.wustl.edu/genome/celegans/microarray/ma_gen_info.cgi), were used for analysis. Log2 ratios (immunopurified RNA over total RNA from extract) were calculated for each gene. Microarrays generated from WS4303 animals were compared to microarrays generated from N2 mock control animals by a Student’s two sample t test.

2012-03-01 | E-GEOD-32941 | 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