Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HVJ-E links Apolipoprotein d to the systemic anti-tumor effects

ABSTRACT: Identification of proteins in close proximity to GFP-Apod proteins using in situ biotinylation technique in Tet GFP-Apod B16F10 cells.

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Hidehisa Takahashi

PROVIDER: PXD043386 | JPOST Repository | Sat Jun 29 00:00:00 BST 2024

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	allSpectra.CID.ITMS.iso_0.apl	Other
	allSpectra.CID.ITMS.iso_1.apl	Other
	allSpectra.CID.ITMS.iso_10.apl	Other
	allSpectra.CID.ITMS.iso_11.apl	Other
	allSpectra.CID.ITMS.iso_12.apl	Other

Items per page:

1 - 5 of 20

Similar Datasets

Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

Project description:Membrane-less subcellular compartments such as cytoplasmic bodies, nuclear bodies, and paraspeckles play important roles in a variety of cellular functions. Although many of the techniques for identifying the components of cellular bodies were developed to address their function, no technique to comprehensively identify the components of these bodies in both static and dynamic states has been established. Here, we developed an antibody-based in situ biotinylation proximity-labeling technique and succeeded in identifying the components of both static and dynamic nuclear bodies, nucleolus and γH2AX foci, respectively. Using this technique, we comprehensively identified the components of Cajal bodies (CBs), including DNAs, RNAs, and proteins, and clarified their interactome in CBs. Furthermore, we captured the dynamic change of CBs by inhibiting transcription. Our analysis revealed that nascent snRNAs transcribed in CBs play a role in CB nucleation through assembling RNA binding proteins, including FTD-related proteins, RBMs and HNRNPs.

2024-10-01 | GSE235853 | GEO

Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

2024-07-06 | PXD043574 | JPOST Repository

Analysis of NF186 proximity proteomes across neuronal development using Nfasc antibodies in an antibody-directed proximity biotinylation strategy combined with mass spectrometry

Project description:Axon initial segment (AIS) cell surface proteins mediate key biological processes in neurons including action potential initiation and axo-axonic synapse formation. However, few AIS cell surface proteins have been identified. Here, we used antibody-directed proximity biotinylation to define the cell surface proteins in close proximity to the AIS cell adhesion molecule Neurofascin.

2023-10-05 | PXD043805 | Pride

mu-crystallin interactome in vivo

Project description:To identify how mu-crystallin operates within striatal astrocytes, we used proximity-dependent biotinylation with BioID2 to identify mu-crystallin interacting proteins relative to GFP controls. Strong biotinylation in vivo permitted identification of the 78-protein mu-crystallin interactome, which will be fully reported in a following publication

2024-01-08 | PXD040991 | Pride

Identification of the Tau aggresome in progressive supranuclear palsy by in situ biotinylation by antibody recognition

Project description:Here, we used an unbiased proteomic approach, which combines antibody-mediated proximity-detection of co-aggregated proteins together with mass spectrometry. Biotinylation by antibody recognition (BAR) is a recently developed method, by which a primary antibody recognises the target of interest in fixed samples. A secondary antibody conjugated to horseradish peroxidase (HRP) recognises the primary antibody, and with the addition of biotin phenol and hydrogen peroxide, facilitates biotinylation of proteins in close proximity. Biotinylated proteins are then biochemically isolated and identified using mass spectrometry (MS).

2023-02-27 | PXD028237 | Pride

Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

Project description:Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

| PRJNA987706 | ENA

CUT&Tag and BioCUT&Tag enables investigation of the AT-rich and dynamic epigenome of Plasmodium falciparum from low input samples

Project description:This study aimed to adapt CUT&Tag to Plasmodium falciparum samples as an efficient and sensitive alternative to classical ChIP-sequencing. We compare H3K9me3 and HP1 CUT&Tag with ChIP-seq datasets, showing successful establishment of CUT&Tag in P. falciparum. Next we aimed to scale down required input material for our CUT&Tag reactions and generated high-quality HP1 tracks with as little as 10.000 nuclei. To minimise potential sample loss we tested feasibility of utilising (frozen) saponin parasite isolates as input material instead of nuclei, which proved to be viable. Lastly, we deployed our new technique Dimerisation-induced Biotinylation-CUT&Tag (DiBioCUT&Tag) to catch transient interactions by biotinylation of strongly associated proteins such as histones. We tested this technique on HP1 and compared standart CUT&Tag with DiBioCUT&Tag. Furthermore, we explored interactions of the transcription factor BDP5, which we were previously unable to succesfully ChIP.

2024-06-27 | GSE270104 | GEO

Promoter targeted histone acetylation of chromatinized parvoviral genome is essential for infrection progress

Project description:The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that at late infection parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e. histone H3 lysine acetylation (H3K27ac). The H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized parvoviral genome, particularly the two viral promoters were rich in H3K27ac. Histone acetyltransferase (HAT) inhibitorefficiently interfered with expression of viral proteins and infection progress. Altogether, our data suggest that acetylation of histones on parvoviral DNA is essential for viral gene expression and completion of viral life cycle.

2016-02-11 | GSE77785 | GEO

Intricate structure of the interphase chromocenter revealed by proximity based biotinylation

Project description:Intricate structure of the interphase chromocenter revealed by proximity based biotinylation

| PRJNA564796 | ENA

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP ChIP]

Project description:Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localized in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.

2024-08-22 | GSE217562 | GEO

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