Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BioID2 interactome of wild-type SYCP1 versus the D918–942 mutant

ABSTRACT: This dataset comprises a tandem mass tag (TMT)–based quantitative proteomic analysis of proteins proximal to SYCP1 identified using BioID proximity labelling. Two independent BioID experiments were performed using distinct SYCP1 constructs: an N-terminal Myc-tagged SYCP1 and a C-terminal HA-tagged SYCP1. For each construct, full-length wild-type SYCP1, a SYCP1 deletion mutant lacking amino acids 918–942, and a SYCP1 knockout negative control were analysed in MCF7 cells. Biotinylated proteins were enriched by streptavidin-based affinity purification, and the resulting protein lysates were submitted to the EMBL Proteomics Core Facility for downstream processing and LC–MS/MS analysis, enabling quantitative comparison of SYCP1-associated proteins across constructs and conditions.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Frank Stein

LAB HEAD: Dr. Urszula McClurg

PROVIDER: PXD072359 | Pride | 2026-04-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2024-08-26-decoys-contam-UP000005640_HomoSapiens_ID9606_20594entries_26102022_dl11012023.fasta.fas	Fasta
	HAtag_FragPipe_workflow.workflow	Other
	HAtag_Set1_ion.tsv	Tabular
	HAtag_Set1_peptide.tsv	Tabular
	HAtag_Set1_protein.tsv	Tabular

Items per page:

1 - 5 of 32

Similar Datasets

BioID-screening reveals the Alk “proximitome” of the Drosophila brain

Project description:Anaplastic lymphoma kinase (Alk) is an evolutionary conserved receptor tyrosine kinase of the insulin receptor family. In addition to its well-studied role in cancer, numerous studies on invertebrate and vertebrate models reveal that Alk-signaling is associated with a variety of complex traits such as: regulation of growth and metabolism, hibernation, regulation of neurotransmitters, synaptic coupling, axon targeting, decision making, memory formation and learning, alcohol use disorder, as well as steroid hormone metabolism. To shed light on ALK-driven signaling processes, we used BioID-based in vivo proximity labeling to reveal the molecules that interact with Alk in the Drosophila CNS. Therefore, we generated first and next generation BioID fusion proteins in the endogenous Alk locus by CRISPR/Cas9 induced homology-directed repair (HDR) resulting in viable and fertile flies. Our results show (i) that the next generation of BioID proteins (TurboID and miniTurbo) outperform the first generation BirA* fusion in terms of labeling efficiency, and (ii) allow identification of proximitomes without overexpression which are likely to be more physiologically relevant. LC-MS/MS-based BioID screening of the larval brain revealed an extensive neuronal Alk-proximitome identifying numerous novel potential components of Alk signaling complexes. Validation of Alk-proximitome candidates further revealed co-expression with Alk in the CNS.

2025-08-22 | PXD026196 | Pride

Immunoisolation of the trypanosome decapping enzyme ALPH1 delivers a potential subcomplex

Project description:Removal of mRNA 5’ caps primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme DCP2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5´-3´exoribonuclease Xrn1. Kinetoplastida lack DCP2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. The enzyme is composed of a catalytic domain flanked by C-terminal and N-terminal extensions. In our related deposition PXD038550 we analysed the ALPH1 interactome by BioID proximity labelling for the full length protein and truncated versions in order to assign domain specific interactions. We showed that Trypanosoma brucei ALPH1 acts in a complex composed of the trypanosome XRN1 ortholog XRNA and four proteins that are unique to Kinetoplastida. The interactome was validated by reverse experiments targeting T. brucei and T. cruzi XRNA by affinity capture and, additionally, the ALPH1 interacting CMGC-family kinase by BioID. Here we carried out affinity capture with T. brucei and T. cruzi ALPH1, which delivers a potential sub-complex missing the C-terminal interactor XRNA.

2023-06-14 | PXD042322 | Pride

Affinity purification MS of human Ubiquitin-tagged RIT1

Project description:Human RIT1 was tagged with HA tag + N or C terminal ubiquitin (HA-Ubiqutin-RIT1 and HA-RIT1-Ubiqutin) and compared with empty vector (EV) or S35N/M90I RIT1 mutant (HA-RIT1 S35N/M90I). The constructs were expressed in human 293T cells and affinity purified using HA beads. RIT1 interacting proteins were compared by quantifying MS1 extracted chromatograms of peptides identified in conventional target-decoy database search.

2024-07-09 | PXD047228 | Pride

Identifying RasGAP SH2 binding partners in Drosophila using mass spectrometry

Project description:Drosophila S2 cells were transfected with RasGAP(WT), RasGAP(SH2*32*) and GFP control. 4 mg of S2 cell lysate was used to pulldown LAP and GFP tagged constructs using GFP-Trap. The pulled down fraction was loaded on SDS-PAGE gels and coomassie stained before several bands (a-u) from two independent but parallel experiments were excised and subjected to MS analysis.

2014-05-20 | PXD000176 | Pride

Determination of the protein interactome of the transcription factor Sox2 in embryonic stem cells engineered for inducible expression of four reprogramming factors

Project description:Coordinate expression of the somatic cell reprogramming factors Oct4, Sox2, Klf4 and c-Myc within embryonic stem cells preserves the self-renewal of these cells, while allowing for the expression epitope tagged Sox2. Taking advantage of this observation, we engineered embryonic stem cells (i-OSKM-ESC) to inducibly express Oct4, Klf4, c-Myc and an epitope tagged form of Sox2 from a polycistronic element, in the presence of doxycycline. We isolated Sox2 and its associated protein complexes by co-immunoprecipitation. Subsequently, we identified the Sox2-protein interactome in self-renewing embryonic stem cells using an unbiased proteomic screen (Multidimensional Protein Identification Technology [MudPIT]). Affymetrix microarrays were used to characterize the gene expression profile of i-OSKM-ESC in the absence and presence of doxycycline. Mouse embryonic stem cells (KH2) were engineered to express Oct4, epitope tagged Sox2, Klf4 and c-Myc in the presence of doxycyline, to produce i-OSKM-ESC. The i-OSKM-ESC were cultured in the absence or presence of doxycyline (4 Âµg/mL) for 24 hours. RNA was extracted from each condition, and used for microarray analysis.

2012-02-20 | E-GEOD-34801 | biostudies-arrayexpress

A unique mRNA decapping complex in trypanosomes

Project description:Removal of mRNA 5’ caps primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme DCP2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5´-3´exoribonuclease Xrn1. Kinetoplastida lack DCP2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. The enzyme is composed of a catalytic domain flanked by C-terminal and N-terminal extensions. Here we analyse the ALPH1 interactome by BioID proximity labelling for the full length protein and truncated versions in order to assign domain specific interactions. We show that Trypanosoma brucei ALPH1 acts in a complex composed of the trypanosome XRN1 ortholog XRNA and four proteins that are unique to Kinetoplastida.The interactome is validated by reverse experiments targeting T. brucei and T. cruzi XRNA by affinity capture and, additionally, the ALPH1 interacting CMGC-family kinase by BioID.

2023-06-14 | PXD038550 | Pride

VZV BioID

Project description:VZV BioID

| PRJEB109045 | ENA

Activation of endogenous retroviruses and induction of viral mimicry by MEK1/2 inhibition in pancreatic cancer

Project description:While pancreatic ductal adenocarcinomas (PDAC) are addicted to KRAS-activating mutations, inhibitors of downstream effectors in the KRAS pathway, such as the clinically approved MEK1/2 kinases inhibitor Trametinib, are devoid of significant therapeutic effects. Nevertheless, the extensive rewiring of regulatory circuits driven by the attenuation of the KRAS pathway can induce novel functional states and vulnerabilities of potential therapeutic relevance. Here, we performed a quantitative histone post-translatinal modification analysis of PDAC cells in the initial hours after MEK1/2 inhibition by Trametinib.

2024-06-16 | PXD043559 | Pride

snRNA data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs

Project description:Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000.

2025-03-15 | E-MTAB-14889 | biostudies-arrayexpress

Mass spectrometry-based profiling of histone posttranslational modifications in uveal melanoma tissue, human melanocytes, and uveal melanoma cell lines

Project description:Purpose: Epigenetic mechanisms and alterations in uveal melanoma (UM) development are still not well understood. In this pilot study, histone posttranslational modifications (PTMs), which are epigenetic mechanisms regulating gene expression, were analyzed in UM formalin-fixed paraffin-embedded (FFPE) tissues and control tissue as well as in UM cell lines and healthy melanocytes to provide a deeper insight into the pathogenesis of UM and the potentially prognostic relevance of these molecular markers. Methods: FFPE tissue of UM (n=24) and normal choroid (n=4) as well as human UM cell lines (n=7), human skin melanocytes (n=6) and uveal melanocytes (n=2), were analyzed by a quantitative mass spectrometry (MS) approach.

2024-02-14 | PXD043551 | 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