Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HER2 RIME experiment from SK-BR-3

ABSTRACT: RIME targeting ERBB2 (HER2) proteins was performed to compare ERBB2 immunoprecipitation efficiency and the quality of the interactome.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Atsushi Yokoyama

PROVIDER: PXD058365 | JPOST Repository | Tue Sep 09 00:00:00 BST 2025

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	37_Sawatsubashi_1_IgG_FusionIT.mzid	Mzid
	37_Sawatsubashi_1_IgG_FusionIT.raw	Raw
	39_Sawatsubashi_2_DAKO_FusionIT.raw	Raw
	41_Sawatsubashi_3_abcam_FusionIT.raw	Raw
	87_Sawatsubashi_4_0308_4_ST_FusionIT.raw	Raw

Items per page:

1 - 5 of 5

Publications

HER2 Interactome Profiling Reveals MARCKS as a Candidate Marker Associated with Aggressive Breast Cancer.

Yokoyama Atsushi A Sawatsubashi Shun S Ebata Akiko A Miki Yasuhiro Y Otsubo Yuri Y Suzuki Takashi T

Cancers 20250902 17

<b>Background/Objectives:</b> HER2, a critical diagnostic marker and therapeutic target in breast cancer, is a membrane receptor that forms diverse signaling complexes, the constituents of which have not been fully characterized in actual breast cancer tissues. <b>Methods:</b> In this study, we applied the Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins (RIME) method, originally developed to explore transcription factor complexes, to identify the complexes formed by HER2 in HE ...[more]

PMID: 40940979

Similar Datasets

HER2 RIME experiment from breast cancer specimen

Project description:RIME targeting ERBB2 (HER2) proteins was performed to analyse ERBB2 interactome to screen novel breast cancer diagnostic markers.

2025-09-09 | PXD061456 | JPOST Repository

HER2 RIME experiment from breast cancer specimen 2

Project description:RIME targeting ERBB2 (HER2) proteins was performed to analyse ERBB2 interactome to screen novel breast cancer diagnostic markers.

2025-09-09 | PXD066103 | JPOST Repository

Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha

Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.

2019-03-21 | PXD012930 | Pride

Androgen receptor RIME using LNCaP cells

Project description:Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) was conducted to examine interactome of androgen receptor (AR) in LNCaP cells.

2021-09-10 | PXD024030 | JPOST Repository

Androgen receptor RIME in prostate cancer cells

Project description:Androgen receptor (AR) is a master transcription factor that drives prostate cancer (PCa) development and progression. Alterations in the expression or activity of AR coregulators significantly impact the disease's outcome. To identify all the essential components of the AR coregulator complex, we utilized a proteomic approach called rapid immunoprecipitation of endogenous proteins (RIME) to systematically identify all coregulator proteins of the AR interactome in PCa cells.

2022-07-12 | PXD031273 | Pride

ER-RIME in wt-MCF7 and MCF7-LTED

Project description:Wild type (wt) MCF7 cells, modelling breast cancer at primary diagnosis, were cultured in phenol red-free RPMI supplemented with 10% FBS and 1nM estradiol (E2). Long-term oestrogen deprived (LTED) cell lines, which model resistance to endocrine therapy, were cultured in phenol red-free RPMI in the absence of exogenous E2 and supplemented with 10% dextran charcoal-stripped bovine serum (DCC). Samples were harvested at baseline and at the point of resistance (LTED). In order to do comparative analysis in the ER-interactome of wt-MCF7 and MCF7-LTED cells, ER-RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins) was conducted in these cells.

2020-07-13 | PXD004648 | Pride

Protein interactome profiling of ER alpha by RIME assay from the human hepatocellular cancer HepG2 stable cells

Project description:Estrogeh insensitivity syndrome (EIS) arises from rare mutations in ERα resulting in the inability of estrogen to exert its biological effects. Due to the rarity, mutations in ESR1 gene and the underlying molecular mechanisms of EIS have not been thoroughly studied. We used RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins) analysis to compare the interactions for ER alpha between the WT ER alpha and Q375H clinical mutant in HepG2 stable cells.

2021-09-09 | PXD020666 | Pride

RIME Analysis of HNF4A binding partners in the intestinal epithelium

Project description:The mechanisms driving gene expression changes during intestinal differentiation are unclear. Our studies have shown differential recruitment and occupancy of Pol II to be a major driver of these gene expression changes. Additionally, we have identified the transcription factor HNF4 as a key player in shaping this phenomenon. To gain insights into the protein-based mechanisms underlying HNF4-mediated Pol II recruitment, we performed RIME (Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins) using anti-HNF4A antibodies in primary mouse epithelium.

2023-10-09 | MSV000093071 | MassIVE

Chromatome of AR and SUMO2/3 idenitified with RIME

Project description:We identifyied AR and SUMO2/3 chromatomes in castration-resistant prostate cancer cells (VCaP) and studied the impact on SUMOylation inhibition (SUMOi)on them utilizing small molecule inhibitor ML792. Chromatome members were identifyied with Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins (RIME) in absence and presence of androgen and ML792. Mass spectrometry analyses were executed with high resolution mass spectrometry LC-MS analysis was performed by using the Evosep One liquid chromatography system coupled to a hybrid trapped ion mobility quadrupole TOF mass spectrometer (Bruker timsTOF Pro) via a CaptiveSpray nano-electrospray ion source. High-confidence chromatome members discriminated from background with SAINT analysis.

2024-08-08 | PXD039179 | Pride

Comparative shotgun proteomics in wt-SUM44 and SUM44-LTED, using RIME and dimethyl-labelling

Project description:Wild type (wt) SUM44 cells, modelling breast cancer at primary diagnosis, were cultured in phenol red-free RPMI supplemented with 10% FBS and 1nM estradiol (E2). Long-term oestrogen deprived (LTED) cell lines, which model resistance to endocrine therapy, were cultured in phenol red-free RPMI in the absence of exogenous E2 and supplemented with 10% dextran charcoal-stripped bovine serum (DCC). Samples were harvested at baseline and at the point of resistance (LTED). To reveal differential protein abundances between wt-SUM44 and SUM44-LTED, the peptides were labelled with dimethyl labelling and underwent fractionation using OFFGEL electrophoresis. In order to reveal the ER-interactome, RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins) was conducted in wt-SUM44 and SUM44-LTED.

2017-12-11 | PXD004807 | 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