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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
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
TranscriptomicsComparison of spheroid-based 3-dimensional culture to monolayer of larynx carcinoma cell line HLaC78.
In vitro proliferation and/or invasion tests (such as MTT assay, Boyden Chamber Assay, Scratch assay) using established and well-characterized cell lines can provide easy and reproducible tools to investigate anti-tumour or anti-invasion agents ex vivo. However, in vivo cells in a tissue context int...
ORGANISM(S): Homo sapiens 
2016-03-11 | E-GEOD-67495 | biostudies-arrayexpress
TranscriptomicsMadin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.
In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-soli...
ORGANISM(S): Canis lupus familiaris 
2013-06-03 | E-GEOD-28381 | biostudies-arrayexpress
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
TranscriptomicsExpression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture
3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture. Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radiore...
ORGANISM(S): Homo sapiens 
2010-07-30 | E-GEOD-17347 | biostudies-arrayexpress
MetabolomicsMetabolic Dynamics in Escherichia coli-Based Cell-Free Systems
The field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metaboli...
2023-02-22 | MTBLS2630 | MetaboLights
MetabolomicsMetabolic Profiling of Escherichia coli-Based Cell-Free Expression Systems for Process Optimization
Biotechnology has transformed the production of various chemicals and pharmaceuticals due to its efficient and selective processes, but it is inherently limited by its use of live cells as 'biocatalysts.' Cell-free expression (CFE) systems, which use a protein lysate isolated from whole cells, have ...
2020-06-02 | MTBLS1079 | MetaboLights
ProteomicsOptimising a self-assembling peptide hydrogel as a Matrigel alternative for 3-dimensional mammary epithelial cell culture
Three-dimensional (3D) organoid models have been instrumental in understanding molecular mechanisms responsible for many cellular processes and diseases. However, established organic biomaterial scaffolds used for 3D hydrogel cultures, such as Matrigel, are biochemically complex and display signific...
ORGANISM(S): Homo sapiens (Human) 
2024-05-22 | PXD045193 | Pride
Mammary epithelial cell 3d Laminin Organoid 
TranscriptomicsRNA-seq of human cancer cell lines HCT116, T47D and A549 in 3D collagen I microenvironments compared to 2D cell culture
The behavior of cancer cells strongly relies on the properties of the extracellular microenvironment. The aim was to compare the whole transcriptome of three non-invasive cancer cell lines, HCT-116, A549 and T-47D, embedded in collagen I matrices in a time-dependent manner to standard two-dimensiona...
ORGANISM(S): Homo sapiens 
2026-07-31 | E-MTAB-16838 | biostudies-arrayexpress
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