Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Co-immunoprecipitation of GFP-Snx33

ABSTRACT: In this project we aimed at identifying proteins interacting with Snx33. For this purpose, we have generated a Snx33 knockout cell lines with GFP-tagged full length Snx33 and GFP-tagged truncation of Snx33: dPXBAR (1-214aa) and PXBAR (159-574aa).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture, Neutrophil

SUBMITTER: Frank Stein

LAB HEAD: Alba Diz-Munoz

PROVIDER: PXD033666 | Pride | 2023-06-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F114357.dat	Other
	Lara_220330_P2048_JS_ES_TMT12_1of60_R1.raw	Raw
	P2048_Lara_220330_P2048_JS_ES_TMT12_1of60_R1_results_20220401_1242_peptides.txt	Txt
	P2048_Lara_220330_P2048_JS_ES_TMT12_1of60_R1_results_20220401_1242_proteins.txt	Txt
	P2048_Lara_220330_P2048_JS_ES_TMT12_1of60_R1_results_20220401_1242_summary.txt	Txt

Items per page:

1 - 5 of 6

Similar Datasets

phospho-proteomic data on the LATS1 interactome from cells treated with two proapoptotic signals: FAS and etoposide

Project description:Using this approach, we obtained phospho-proteomic data on the LATS1 interactome from cells treated with two proapoptotic signals: FAS and etoposide, which both activate LATS kinase activity [28].To identify the LATS1 interactome we transiently expressed GFP-LATS1 in HeLa cells, immunoprecipitated GFP-LATS1 with anti-GFP antibodies and identified the associated proteins using mass-spectrometry. Unspecific binding proteins were discarded by comparing with the control GFP IP.

2021-09-09 | PXD018903 | Pride

Identification of novel Coronin 1A interacting proteins

Project description:Severe combined immunodeficiency 8 (IMD8) is caused by mutations in the human Coronin 1A (Coro1A). The clinical presentation of IMD8 patients is characterized by recurrent bacterial infections, suggesting an important role of Coro1A in innate immunity. To analyze the molecular mechanism of Coro1A during neutrophil recruitment, we identified the Coro1A interactome by conducting co-immunoprecipitation (Co-IP) experiments using GFP NanoTrap technology and subsequent mass spectrometry (LC-MS/MS) using human neutrophil-like differentiated HL-60 (dHL-60) cells stably expressing Coro1A-EGFP (dHL-60-Coro1A-EGFP) cells.

2017-06-29 | PXD004635 | Pride

Comprehensive cross-linking mass spectrometry reveals molecular insights into the between peripheral and core NuRD complex subunits

Project description:Affinity purifications of CHD4 and CDK2AP2 to identify their interactors. The C-terminally tagged CHD4 has a C-terminal truncation to test whether this domain is required for the interaction with other NuRD subunits. GFP-purifications of both N- and C-terminally tagged CDK2AP2 were performed.

2020-12-07 | PXD017378 | Pride

GFP pulldown for the RiboVD project

Project description:GFP-tagged viral peptide sequences and their controls were used to pull down interactors from human (uninfected) or green monkey (viral infected) cell lysate. After sample preparation, digestion and bottom-up LC-MS/MS analysis, the enriched proteins were identified.

2023-03-09 | PXD033874 | Pride

greenCUT&RUN: a rapid and efficient genome profiling approach for transcription and chromatin regulatory proteins

Project description:Chromatin modifiers, transcription factors and cofactors regulate gene expression through engagement with chromatin and DNA, which can be detected by a variety of genomic techniques. Here, we describe a novel method ‘greenCUT&RUN’ for genome-wide profiling of transcription regulatory factors, which has higher sensitivity, resolution, accuracy and reproducibility than existing methods, whilst assuring specificity as assessed for the gene specific transcription factors NFY and c-FOS, and for the basal transcription factor TBP. Our strategy begins with tagging the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. Since the nanobody targets GFP, the greenCUT&RUN approach eliminates dependency on protein-specific antibodies, which makes it widely applicable. To examine, if GFP-tagged proteins form complex with known interactors and GFP did not interfere in the formation of protein complex, mass spectrometry was performed.

2021-01-13 | PXD021089 | Pride

LARP iCLIP in MDAMB231 cell lines

Project description:This experiment aims to globally identify LARP6 binding sites on the transcriptome by performing iCLIP in MDA-MB231 cell lines expressing GFP-LARP6. MDA-MB231 cell lines expressing GFP only were used as controls in the experiment.

2020-11-01 | E-MTAB-9636 | biostudies-arrayexpress

Human WIPI interactome (LC-MSMS)

Project description:Analysis of the WIPI protein interactome using nanoLC-MS/MS analysis upon the immunopurification of GFP-tagged WIPI1, WIPI2B, WIPI2D, WIPI3, WIPI4 and GFP alone from U2OS cells. Prior to immunopurifications, cells were either kept under fed (DMEM/FCS) or starved conditions (EBSS), or were treated with wortmannin (200 nM) for 3 h.

2017-06-01 | PXD006119 | Pride

Molecular characterisation of the SL1 snRNP and other factors involved in spliced leader trans-splicing in the nematode Caenorhabditis elegans using immunoprecipitation and LC-MS/MS.

Project description:Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the factors involved in this reaction are not well known. Here we perform a molecular analysis of key components in this reaction by immunoprecipitation of GFP-tagged SNA-1 and SNA-3 proteins from C. elegans embryonic extracts treated with/without RNAseA/T1 followed by the identification of associated proteins using LC-MS/MS and label-free quantification. As control, embryonic extract from wild type N2 animals were also subjected to the same treatment. Note file names (e.g. PE906_SNA1_RNase_IP_anti-GFP_beads) indicate the name of the C. elegans line (PE906_), the name of the protein tagged with GFP (SNA1) and whether samples were treated with RNases A and T1 (RNase), and for raw files whether immunoprecipitation was done with anti-GFP nanobody coupled agarose beads (IP_anti_GFP_beads), or control agarose beads (IP_control_beads), respectively. Note that SNA-3 protein is only identified by its Uniprot identifier Q9GYR5.

2022-06-24 | PXD024763 | Pride

Complementary proteomics strategies identify the ataxin-1 interactome in Neuro-2a cells

Project description:To identify protein partners of ataxin-1 in neuronal cells under control or stress conditions, we use complementary proteomics strategies of proximity-dependent biotin identification (BioID) and affinity purification (via GFP-trap pulldown) in Neuro-2a cells expressing epitope-tagged forms of ataxin-1[85Q]. These approaches allowed our enrichment of proximal proteins and interacting partners, respectively, with the subsequent protein identification performed by liquid chromatography-MS/MS. Background proteins, defined by identification not dependent on the polyQ-ataxin-1 protein, were additionally identified by their endogenous biotinylation (for the BioID protocol) or by their non-specific interaction with GFP only (in the GFP-trap protocol). All datasets were generated from biological replicates.

2018-10-18 | PXD010352 | Pride

Identification of ETO2-GLIS2 targets by ChIP-sequencing

Project description:Acute megakaryoblastic leukemia (AMKL) is a subtype of leukemia primarily diagnosed in childhood and generally associated with poor prognosis. Genetic alterations found in de novo childhood AMKL include the OTT-MAL fusion, MLL and NUP98 fusions and the recently identified ETO2-GLIS2 fusion that involves two transcriptional regulators. In order to identify ETO2-GLIS2-bound regions as well as the chromatin landscape in human AMKL cells, we performed ChIP-seq analyses in AMKL MO7E cell line and in AMKL patient derived cells. Since existing GLIS2 antibodies could not successfully pull-down ETO2-GLIS2, we introduced the GFP at the endogenous GLIS2 loci in the MO7E cell line using a CRISPR/Cas9 approach to obtain physiological expression of a GFP-tagged ETO2-GLIS2 (MO7e-KI cell line). ChIP-seq were performed using antibody against GFP and ETO2 to identify ETO2-GLIS2-bound regions, against ERG to investigate colocalization and against chromatin marks to highlight repressed (H3K27me3) and active (H3K4me3: promoters; H3K27Ac, H3K4me1: enhancers) regions.

2017-05-22 | E-MTAB-4367 | 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