Dataset Information

BAD3SA BioID in 2D and 3D MCF10A cell culture

ABSTRACT: BioID proximity labeling experiment on bait protein Bcl2-associated agonist of cell death (BAD) with three serine to alanine mutations (S75A, S99A, S118A) in MCF10A cell culture stably expressing BAD-miniTurbo. 2D cell culture: 20220805; sample: BAD3SA-turbo-biotin; control: BAD3SA-turbo (n=3); other raw files in the experiment (BAD-turbo-biotin, BAD-biotin, turbo-biotin, BAD-turbo) are found under the identifier MSV000093357. The file "20230921-2D-miniTurbo-BAD3SA-low-abundance-imputation.pdResult" contains the Proteome Discoverer search result for the full 2D miniTurbo experiment. 3D cell culture: 20230710; sample: BAD3SA-biotin (n=4); other raw files (BAD-turbo-biotin, turbo-biotin) in the experiment are found under the identifier MSV000093358. The file "20230921-3D-miniTurbo-BAD3SA-low-abundance-sampling.pdResult" contains the Proteome Discoverer search result for the full 3D miniTurbo experiment.

INSTRUMENT(S): Orbitrap Fusion Lumos

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

SUBMITTER: Ing Swie Goping Olivier Julien

PROVIDER: MSV000100167 | MassIVE | Tue Dec 09 14:34:00 GMT 2025

SECONDARY ACCESSION(S): PXD071781

REPOSITORIES: MassIVE

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three-dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two-dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a hepatocellular carcinoma (HCC) model that enables cellular maintenance in a polycarbonate scaffold structure. Albumin, regarded as a differentiation marker, was elevated in statically 3D cultivated HepG2 cells. Expression of HCC tumor marker alpha-fetoprotein (AFP) was reduced compared to immunofluorescence stainings of 2D cultivated cells. Remarkably, expression of cytokeratin and pathophysiologically relevant beta-1 integrin (ITGB1) was found enhanced in nonperfused 3D cell culture. Changes in gene expression induced by the 3D cultivation environment were investigated using Ingenuity Pathway Analysis (IPA). Our findings revealed involvement of the insulin growth factor (IGF) signaling pathway in upregulation of matrix metalloproteinases (MMP) and ITGB1. The experimental data indicate a more differentiated state in 3D cultivated HepG2 cells than in the respective 2D experiments. Hence, scaffold-supported 3D cultivation of HepG2 cells may lead to a gain of information valuable for both drug testing and cancer research. HepG2 cells were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25x10^6 cells in 2D and with 1x10^6 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D, i.e., monolayer cultures, 3D, i.e., statical 3D cultures and BR, which denotes perfused 3D culture of HepG2 cells. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate-based microporous cellular support. For 3D static cultivation, cell-inoculated MatriGrids were placed in wells of a 24-well plate. Microarray experiments of three 2D (i.e., control), three 3D statically and three actively perfused 3D cultivations were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturer's instructions (Illumina, San Diego, CA). Altogether, 9 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.

Dataset Information

BAD3SA BioID in 2D and 3D MCF10A cell culture

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets