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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Global expression of mouse hepatocytes cultured as monolayers or as three-dimensional aggregates

ABSTRACT: Three-dimensional (3D) culture of hepatocytes leads to improved and prolonged synthetic and metabolic functions, but the underlying molecular mechanisms were unknown. In order to investigate the molecular mechanisms underlying 3D cell-cell interactions in maintaining hepatocyte differentiated functions ex vivo, microarray analyses were performed on primary mouse hepatocytes cultured either as monolayers on tissue culture dishes (TCD) or as 3D aggregates in rotating wall vessel (RWV) bioreactors. Primary hepatocytes were isolated from mice and cultured on TCDs or within RWVs for 4 hours or 24 hours. Freshly isolated hepatocytes (t0) were used as baseline controls. Each experimental condition has three independent biological replicates.

ORGANISM(S): Mus musculus

SUBMITTER: Tammy Chang

PROVIDER: E-GEOD-53054 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global expression of mouse hepatocytes cultured as monolayers or as three-dimensional aggregates

Project description:Three-dimensional (3D) culture of hepatocytes leads to improved and prolonged synthetic and metabolic functions, but the underlying molecular mechanisms were unknown. In order to investigate the molecular mechanisms underlying 3D cell-cell interactions in maintaining hepatocyte differentiated functions ex vivo, microarray analyses were performed on primary mouse hepatocytes cultured either as monolayers on tissue culture dishes (TCD) or as 3D aggregates in rotating wall vessel (RWV) bioreactors.

2013-12-23 | GSE53054 | GEO

Gene expression profiling of primary human bone marrow mesenchymal stromal cells (MSCs) cultured as 2D monolayers and 3D cellular aggregates (spheroids)

Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.

2015-09-30 | E-MTAB-3795 | biostudies-arrayexpress

Role of Ror2 in primordial germ cell migration

Project description:Primordial germ cells (PGCs), the embryonic precursors of eggs and sperm, are a unique model for identifying and studying regulatory mechanisms in singly migrating cells. From their time of specification to eventual colonization of the gonad, mouse PGCs traverse through and interact with many different cell types, including epithelial cells and mesenchymal tissues. Work in drosophila and zebrafish have identified many genes and signaling pathways involved in PGC migration, but little is known about this process in mammals. We have generated a point mutation in the Ror2 gene that we know disrupts primordial germ cell migration in the developing mouse embryo. We used microarray analysis to determine if this defect is mediated through genome-wide or pathway-specific transcriptional changes. We analyzed primordial germ cells (PGCs) from 4 wild-type (WT) and 4 Ror2Y324C/Y324C mutant embryos using Oct4-DPE-EGFP. PGCs were collected during their active migratory state at embryonic day 9.5 (somite range 20-25).

2014-08-08 | E-GEOD-60179 | biostudies-arrayexpress

FRT thyroid cells: 2D monolayers vs. 3D follicles

Project description:Transcriptional profiling of the Fischer Rat Thyroid (FRT) cells comparing polarizing cells grown as a confluent two-dimensional monolayer (2D culture system) with cells grown in matrigel where they acquire a three-dimensional follicular structure (3D culture system).The goal was to identify regulators of 3D epithelial thyroid polarization and follicle formation.

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Human bone marrow stromal cells under simulated microgravity ' bottom-up, label free, shot gun approach in DIA

Project description:A multidisciplinary approach was employed to characterize morphological, biochemical and molecular changes underlying the human BMSCs response to simulated microgravity exposure during osteogenic differentiation.

2022-10-02 | PXD033475 | Pride

Transcription profiling of human umblical vein endothelial cells (HUVEC) undergoing tubulogenesis in a 3D fribrin matrix or cultured as monolayers

Project description:In order to determine genes that are differentially expressed during angiogenesis, Human Umbilical Vein Endothelial Cells (HUVEC) were cultured as 3D cultures undergoing tubulogenesis in a 3D fibrin matrix, or cultured as monolayers on top of a 3D fibrin matrix. RNA was then collected, reverse transcribed to cDNA and hybridized to glass slide oligo arrays containing 19k human genes. Differentially expressed genes in HUVECs undergoing tubulogenesis were then determined by comparing 2D to 3D culture samples.

2009-10-29 | E-MEXP-2410 | biostudies-arrayexpress

Gene expression in a three dimensionally cultivated human hepatocytes

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 3D hepatocyte cell culture that enables cellular maintenance in a polycarbonate scaffold structure. Our data indicate that an actively perfused three dimensional cell culture displays a more pronounced metabolic genotype than statically cultivated hepatocytes. Human hepatocytes of three donors were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25 x106 in 2D and with 1x 106 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 culture and BR denotes perfused 3D culture of hepatocytes. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate based microporous cellular support. For 3Dstatic cultivation, cell- inoculated MatriGrids were placed in wells of a 24 wells plate. Microarray experiments of three 2D (i.e. control), three 3D statically and three actively perfused 3D cultivations, respectively, were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturerM-bM-^@M-^Ys instructions (Illumina, San Diego, CA). Altogether, 8 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.

2013-03-31 | E-GEOD-44580 | biostudies-arrayexpress

3D culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival

Project description:Full title: Three-dimensional culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival The AIDS-NHL-derived cell line, UMCL01-101, representing diffuse large B-cell lymphoma of immunoblastic morphology (AIDS-IBL), was grown in conventional, static suspension culture or three-dimensionally (3D) in the Rotating Wall Vessel (RWV) bioreactor. The objective was to assess the impact on gene expression of growth as a three-dimensional tissue assembly. Global gene expression analysis was performed on UMCL01-101 cells grown under either condition using Affymetrix microarray. UMCL01-101 cells were cultured in the Rotating Wall Vessel bioreactor to form 3D assemblies, or in conventional suspension culture, for 15 days. RNA was prepared from triplicate samples under each growth condition and submitted for microarray analysis.

2010-03-07 | E-GEOD-18826 | biostudies-arrayexpress

Conditions for maintenance of hepatocyte differentiation and function in 3D cultures

Project description:3D spheroid cultures of primary human hepatocytes (PHH) are used in studies of hepatic drug metabolism and toxicity. However, the 3D spheroids are maintained under different conditions, with possible cofounding results. Here we performed an in-depth analysis of how various culture conditions influence 3D spheroids. Our aim was to find optimal conditions for the maintenance of a normal PHH phenotype.

2022-02-17 | PXD024632 | Pride

Progestin-containing Contraceptives Alter Expression of Host Defense-related Genes of the Endometrium and Cervix

Project description:Epidemiological studies indicate that progestin-containing contraceptives may increase susceptibility to HIV and other infections; however, underlying mechanisms involving the upper female reproductive tract are undefined. To determine the effects of depot medroxyprogesterone acetate (DMPA) and the levonorgestrel intrauterine system (LNG-IUS) on gene expression and physiology of the human endometrial and cervical transformation zone (TZ), microarray analyses were performed on whole tissue biopsies. In endometrium, activated pathways included leukocyte chemotaxis, attachment, and inflammation in DMPA (z>2.5) and LNG-IUS (z>3.5) users, and regulation of pattern recognition receptors and other immune mediators. In cervical TZ, progestin treatment altered expression of tissue remodeling and viability genes, but not those of immune functions. Together, these results indicate that progestins influence expression of immune-related genes in endometrium that would be expected to result in the local recruitment of HIV target cells, and thus may increase HIV susceptibility. It is important to consider the upper reproductive tract in the assessment of effects of contraceptives that may influence susceptibility to pathogens, such as HIV. Cross-sectional study conducted at an academic medical center. Cervical transformation zone and endometrial biopsies were obtained from 3 groups of volunteers: those using no hormonal contraceptives (controls, mid-secretory phase, n=20 cervix, 11 endometrium), DMPA users (150mg, n=15, 8), or LNG-IUS users (n=17, 13). DMPA and LNG-IUS groups had used these contraceptives for at least 6 months.

2014-11-21 | E-GEOD-60129 | biostudies-arrayexpress

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