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ProteomicsLabel-free quantification of 3D MCF10A cell culture proteome (DIA)
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)
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-05-21 | MSV000094825 | MassIVE
MetabolomicsLiquid chromatography coupled to high-resolution mass spectrometry metabolomics: A useful tool for investigating tumor secretome based on a three-dimensional co-culture model

Three-dimensional (3D) cell culture technologies, which more closely mimic the complex microenvironment of tissue, are being increasingly evaluated as a tool for the preclinical screening of clinically promising new molecules, and studying of tissue metabolism. Studies of metabolites released int...

2023-12-12 | MTBLS5375 | MetaboLights
ProteomicsExtracellular vesicles secreted by 3D tumor organoids are enriched for immune regulatory signaling biomolecules compared to conventional 2D glioblastoma cell systems
Background: Newer 3D culturing approaches are a promising way to better mimic the in vivo tumor microenvironment and to study the interactions between the heterogeneous cell populations of glioblastoma multiforme. Like many other tumors, glioblastoma uses extracellular vesicles as an intercellular c...
ORGANISM(S): Homo sapiens (Human) 
2024-04-09 | PXD047328 | Pride
Ev Extracellular vesicle Proteomics Microrna 3d organoid model Brain cancer Glioblastoma multiforme 
ProteomicsSmooth muscle cell spheroids as 3D model of phenotypic plasticity and matrix deposition revealed by 2D-3D proteomics
Our study aims to compare 2D adherent and 3D floating (spheroid) cell cultures of in the context of cellular physiology and in atherosclerosis modelling. Here, we utilize vascular smooth muscle cells from rat aorta to profile 2D and 3D proteomes.
ORGANISM(S): Rattus norvegicus (Rat) 
2026-09-07 | PXD069144 | Pride
Smoot muscle cell  spheroids  3d cell culture  lc-ms/ms 
GenomicsRNA-sequencing of prostate cancer xenografts, their 3D cultures and prostate cancer cell-lines.
RNA-sequencing of prostate cancer xenografts, their 3D cultures and prostate cancer cell-lines.
PRJEB42165 | ENA
GenomicsSpatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
PRJNA530150 | ENA
ProteomicsBAD BioID in 2D MCF10A cell culture
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).
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-11-10 | MSV000093357 | MassIVE
ProteomicsMicroenvironment remodeling during human iPSC-derived NSC 3D differentiation
Brain microenvironment plays an important role in neurodevelopment and function, where extracellular matrix (ECM) components and soluble factors modulate cellular features, as migration, proliferation survival and neuronal function. Disruption of microenvironment’s homeostasis is often related to pa...
ORGANISM(S): Homo sapiens (Human) 
2018-07-31 | PXD007130 | Pride
3d cultures  neual differentiation  hipsc-derived nsc  ecm  microenvironment  swath 
TranscriptomicsGene expression of LNCaP cells grown in 2D cultures and polyethlene glycol-based hydrogels with the presence of synthetic androgen, R1881
Analysis of LNCaP cell molecular differences and their response to R1881 in 2D and 3D cultures. Androgen regulated genes were differentially expressed between 2D and 3D cultures. These results provide insights into factors that influence the expression of androgen regulated genes In this study, LNCa...
ORGANISM(S): Homo sapiens 
2013-02-04 | E-GEOD-33610 | biostudies-arrayexpress
GenomicsPolymer-mediated oligo delivery enables construction of spatially encoded 3D cultures for analysis by single-cell RNA sequencing
Polymer-mediated oligo delivery enables construction of spatially encoded 3D cultures for analysis by single-cell RNA sequencing
PRJNA1028306 | ENA
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