Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression data from C57BL/6 mouse hepatocyte spheroids on days 1, 7 and 14 post spheroid formation.

ABSTRACT: Hepatocytes were isolated from C57BL6/J mice and cryopreserved. Spheroids were generated from cryopreserved hepatocytes by spontaneous self-aggregation in ultra-low attachment 96-well plates. Microarray profiling of the entire transcriptome was performed on spheroids cultured for 1, 7, and 14 days post spheroid formation from N=2 spheriod preparations from each sex. Only 287 of 13,081 total mRNAs detected (2.2%) were differentially expressed in spheroids over time.

ORGANISM(S): Mus musculus

PROVIDER: GSE152173 | GEO | 2021/01/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium

Project description:Immortal spheroids were generated from fetal mouse intestine using the culture system developed to culture organoids from adult intestinal epithelium. Spheroids are made of a monostratified polarized epithelium displaying a poorly differentiated intestinal phenotype. The proportion of spheroids generated from intestinal explants progressively decreases from fetal to postnatal period, with a corresponding increase in production of organoids. Spheroid cells show indefinite self-renewing properties but exhibit a transcriptome strikingly different from that of adult intestinal stem cells reminiscent of incompletely caudalized progenitors. The receptor Lgr4, but not Lgr5, is essential for their growth. Trop2/Tacstd2 and Cnx43/Gja1, two markers highly enriched in spheroids, are expressed throughout the E14 intestinal epithelium. Comparison of in utero and neonatal lineage tracing using Cnx43-CreER and Lgr5-CreERT2 mice identified spheroid-generating cells as developmental progenitors involved in generation of the prenatal intestinal epithelium. Ex vivo, spheroid cells have the potential to differentiate into organoids, thus qualifying them as a new type of intestinal stem-like cells. Two-channel microarray experiments were performed from spheroid/organoid pairs isolated each from a given embryo. Following initial seeding of small intestine from a given embryo/mouse (at E16, E18 or P0), spheroids and organoids were selectively picked up for each animal and replated for 3 passages to reach sample homogeneity. Hybridization was performed on the 4 independent pairs with dye-swap.

2014-01-21 | E-GEOD-49803 | biostudies-arrayexpress

Array CGH analysis of single spheroids from glioblastoma spheroid cultures

Project description:The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures. Keywords: Comparative genomic hybridization We performed array comparative genomic hybridization of spheroid cultures derived from 2 glioblastoma spheroid cultures using as a reference DNA from healthy donors.

2010-05-14 | E-GEOD-14821 | biostudies-arrayexpress

Molecular analysis of glioblastoma stem cell-like spheroid cultures identifies novel tumor-relevant genes

Project description:This SuperSeries is composed of the following subset Series: GSE14818: Gene expression analysis of glioblastoma spheroid cultures I GSE14819: Array CGH analysis of glioblastoma serum grown adherent cultures GSE14820: Array CGH analysis of glioblastoma cell lines GSE14821: Array CGH analysis of single spheroids from glioblastoma spheroid cultures GSE14822: Array CGH analysis of glioblastoma spheroid cultures GSE14823: Array CGH analysis of glioblastomas GSE16666: Gene expression analysis of glioblastoma spheroid cultures II Refer to individual Series

2010-02-12 | E-GEOD-14824 | biostudies-arrayexpress

Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium

2014-01-21 | GSE49803 | GEO

Genomic characterization of ovarian cancer spheroids

Project description:Spheroids are 3D multi-cell aggregates formed in non-addherent culture conditions. In ovarian cancer (OC), they serve as a vehicle for cancer cell dissemination in the peritoneal cavity. We investigated genes and networks upregulated in three dimensional (3D) versus two-dimensional (2D) culture conditions by Affymetrix gene expression profiling and identified ALDH1A1, a cancer stem cell marker as being upregulated in OC spheroids. Network analysis confirmed ALDH1A1 upregulation in spheroids in direct connection with elements of the beta-catenin pathway. A parallel increase in the expression levels of beta-catenin and ALDH1A1 was demonstrated in spheroids vs. monolayers an in successive spheroid generations by using OC cell liness and primary OC cells. The percentage of Aldefluor positive cells was significantly higher in spheroids vs. monolayers in IGROV1, A2780, SKOV3, and primary OC cells. B-catenin knock-down decreased ALDH1A1 expression and chromatin immunoprecipitation demonstrated that beta-catenin directly binds to the ALDH1A1 promoter. Both siRNA mediated beta-catenin knock-down and a novel ALDH1A1 small molecule enzymatic inhibitor described here for the first time, decreased the number of OC spheroids (p<0.001) and cell viability. These data strongly support the role of beta-catenin regulated ALDH1A1 in the maintenance of OC spheroids and of a stem cell phenotype and propose new ALDH1A1 inhibitors targeting this cell population. Different gene profiles were observed in ovarian cancer spheroids versus ovarian cancer monolayers. Nine samples were analyzed in triplicate. Each group is a reference.

2014-01-03 | E-GEOD-53759 | biostudies-arrayexpress

Effect of Trp53 mutations on mouse oviductal epithelial cell spheroids

Project description:To identify mutant p53-dependent pathway alterations that are enhancing spheroid survival properties in mouse oviductal epithelial (OVE) cell lines, we generated OVE4 and OVE16 cell lines with either Trp53 deletion or stable expression of p53R175H. RNA-seq was performed on RNA from OVE spheroids to determine differential gene expression. Gene set enrichment analysis was performed to indentify enriched pathways in parental OVE spheroids compared to spheroids with Trp53 deletion or expression of p53R175H

2023-06-13 | GSE227681 | GEO

Array CGH analysis of single spheroids from glioblastoma spheroid cultures

Project description:The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures. Keywords: Comparative genomic hybridization

2010-02-13 | GSE14821 | GEO

Changes in Global Gene Expression Associated with 3D Structure of Tumors: an ex vivo Matrix-Free Mesothelioma Spheroid Model

Project description:Tumor microenvironments present significant barriers to anti-tumor agents. Molecules involved in multicellular tumor microenvironments, however, are difficult to study ex vivo. Here, we generated a matrix-free tumor spheroid model using the NCI-H226 mesothelioma cell line and compared the gene expression profiles of spheroids and monolayers using microarray analysis. Microarray analysis revealed that 142 probe sets were differentially expressed between tumor spheroids and monolayers. Gene ontology analysis revealed that upregulated genes were primarily related to immune response, wound response, lymphocyte stimulation and response to cytokine stimulation, whereas downregulated genes were primarily associated with apoptosis. Among the 142 genes, 27 are located in the membrane and related to biologic processes of cellular movement, cell-to-cell signaling, cellular growth and proliferation and morphology. Western blot analysis validated elevation of MMP2, BAFF/BLyS/TNFSF13B, RANTES/CCL5 and TNFAIP6/TSG-6 protein expression in spheroids as compared to monolayers. Thus, we have reported the first large scale comparison of the transcriptional profiles using an ex vivo matrix-free spheroid model to identify genes specific to the three-dimensional biological structure of tumors. The method described here can be used for gene expression profiling of tumors other than mesothelioma. We generated a matrix-free tumor spheroid model using the NCI-H226 mesothelioma cell line and compared the gene expression profiles of spheroids and monolayers using microarray analysis. Microarray analysis experiments were performed in triplicates. A total of six samples (three for monolayers and three for spheroids) were analyzed.

2012-06-20 | E-GEOD-37629 | biostudies-arrayexpress

Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model

Project description:To investigate epigenetic dynamics in a 3D liver spheroid model, liver spheroids were treated with sodium butyrate for 3 days and allowed to recover for 1 week. We then performed gene expression profiling analysis using data obtained from RNA-seq of spheroids at 4 time points

2022-09-26 | GSE213944 | GEO

Analysis of citrullination of extracellular matrix proteins in spheroid cultures of fibroblasts and cancer cells

Project description:Eight different human cancer cell lines were cocultured with human cancer associated fibroblasts (CAF) as spheroid cultures. In another setup UT-SCC-7 cutaneous squamous cell carcinoma cells, together with human skin fibroblasts (SFB) and UT-SCC-2 cells together with gingival fibroblasts (GFB) were cultured as spheroid cocultures. These spheroids were treated with PAD4 or with citrullination buffer only. All spheroids were hypotonically lysed, and the remaining insoluble material was digested to peptides and analysed by LC-MS/MS.

2022-11-21 | PXD033555 | Pride

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