Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Label-free quantification of 3D MCF10A cell culture proteome (DIA)

ABSTRACT: Global shotgun proteomic analysis using data independent acquisition (DIA) and Spectronaut analysis on the input cell lysates before the enrichment step in proximity labeling experiments, specifically MCF10A cells stably expressing miniTurbo-BAD in 3D with biotin treatment (n=4)

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Ing Swie Goping Olivier Julien

PROVIDER: MSV000094825 | MassIVE | Tue May 21 16:12:00 BST 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Comparing the BAD Protein Interactomes in 2D and 3D Cell Culture Using Proximity Labeling.

Pirayeshfard Leila L Luo Shu S Githaka John Maringa JM Saini Arashdeep A Touret Nicolas N Goping Ing Swie IS Julien Olivier O

Journal of proteome research 20240703 8

Protein-protein interaction studies using proximity labeling techniques, such as biotin ligase-based BioID, have become integral in understanding cellular processes. Most studies utilize conventional 2D cell culture systems, potentially missing important differences in protein behavior found in 3D tissues. In this study, we investigated the protein-protein interactions of a protein, Bcl-2 Agonist of cell death (BAD), and compared conventional 2D culture conditions to a 3D system, wherein cells w ...[more]

PMID: 38959414

Similar Datasets

Expression profiling of MCF10A cells in 2D and 3D culture

Project description:In these microarray experiments, we characterize the gene expression of mammary epithelial cells (MCF10A cells) grown in either a traditional monolayer cell culture setting (2D) or on Matrigel, which induces single MCF10A cells to form organized acinar structures (3D). Morphogenesis of mammary epithelial cells into organized acinar structures in vitro is accompanied by widespread changes in gene expression patterns, including a substantial decrease in expression of Myc. The purpose of this study was to analyze the impact of morphogenesis and organization on gene expression with respect to changes in overall gene expression and Myc target gene expression. MCF10A cells were cultured in 2D for either 2 or 5 days (3 biological replicates each) or in 3D for 8 or 16 days (3 or 5 biological replicates, respectively)

2011-06-01 | E-GEOD-26148 | biostudies-arrayexpress

Expression profiling of MCF10A cells in 2D and 3D culture

2011-06-01 | GSE26148 | GEO

3D + LY vs. 3D culture of HUASMC

Project description:3D + LY vs. 3D culture of HUASMC

| PRJNA552085 | ENA

Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture

Project description:Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture

| PRJNA491420 | ENA

BAD BioID in 2D MCF10A cell culture

Project description:BioID proximity labeling experiment on Bcl2-associated agonist of cell death (BAD) using BAD-miniTurbo stable cell line in MCF10A, 2D cell culture. Sample: BAD-turbo-biotin; controls: BAD-biotin, turbo-biotin, BAD-turbo (n=3).

2023-11-10 | MSV000093357 | MassIVE

MCF10A-HER2/3 cells grown in 3D cultures in the presence or absence of SHP2

Project description:The first bona fide PTP proto-oncogene was the Src-homology 2 domain-containing phosphatase SHP2 (encoded by PTPN11), an ubiquitously expressed PTP that transduces mitogenic, pro-survival, cell fate and/or pro-migratory signals from numerous growth factor-, cytokine- and extracellular matrix receptors. In malignancies, SHP2 is hyperactivated either downstream of oncoproteins or by mutations.We provide analysis of the mammary epithelial cells MCF10A overexpressing human HER2 and HER3 and grown in 3D cultures for 15 days in the presence or absence of SHP2. The human mammary epithelial cells MCF10A were transduced with a doxycycline-inducible lentiviral vector expressing a CTRL miR or SHP2 miR1 or SHP2 miR2. Cells from each group were grown in 3D cultures, and the knockdown of SHP2 was induced for 15 days. RNA was extracted for gene expression analysis.

2011-12-20 | E-GEOD-34524 | biostudies-arrayexpress

Transcription profiling of human mammary epithelial cells with MycER activation using 4-hydroxytamoxifen following growth in 2D monoloyers with or without EGF and insulin or in 3D Matrigel culture

Project description:MCF10A MycER cells were grown either on 2D monolayer culture in the presence of complete growth medium, in the absence of EGF and insulin or in 3D Matrigel culture for 20 days to form acinar structures. MycER was activated with 4-hydroxytamoxifen (4-OHT) in all samples for 2 or 48 h. Control cells were treated with ethanol. The aim of the study was to explore the effect of different growth conditions on gene expression changes in response to c-Myc activation.

2006-12-31 | E-MEXP-765 | biostudies-arrayexpress

Genome-wide analysis of control and MMP-14 (MT1-MMP) expressing MCF-7 cells growing in three-dimensional (3D) type I collagen gels versus monolayer cell culture conditions

Project description:In order to investigate the impact of MMP-14 (MT1-MMP) and three-dimensional (3D) culture conditions on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (CTRL) or human MMP-14 cDNA (MT1) in monolayer (2D) and 3D collagen (3D Col) growth conditions. MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 24, 48 and 72 hours in three-dimensional (3D) type I collagen gels or in monolayer culture conditions. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 4 independant biological replicates were pooled.

2014-12-15 | E-GEOD-49595 | biostudies-arrayexpress

Predictive Response to Chemotherapy (FOLFOX or FOLFIRI) by ex Vivo Culture 3D Technique in Metastatic Colorectal Cancer

Project description:Prospective, open labelled, multicenter trial to evaluate the feasibility of ex vivo culture 3D (chemogram obtaining) on biopsies in order to estimate the predictive value of this technique for treatment response in patients treated by two different chemotherapies (FOLFOX or FOLFIRI) for colorectal cancer.

| 2221037 | ecrin-mdr-crc

3D + LY vs. 3D culture of HUASMC

Project description:To study the impact of TGF signaling on the transcriptome of vascular smooth muscle cells, we cultured human umbilical artery smooth muscle cells as 3D aggregates in hanging drops for 48 hours. One group was treated with TGFβRI/II inhibitor LY2109761 (10 μM, additional 10 μM after 24 h), the other group with solvent (DMSO) as control. RNA was isolated from both groups after 48h

2019-12-16 | GSE133649 | 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