Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-MEXP-2657

ABSTRACT: Transcription profiling by array of human stromal cells cultured with or without 3D BPH-1 prostate epithelial cells

PROVIDER: E-MEXP-2657 | ExpressionAtlas | 2025-01-22

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-MEXP-2657-analysis-methods.tsv	Tabular
	E-MEXP-2657-atlasExperimentSummary.Rdata	Rdata
	E-MEXP-2657-configuration.xml	Xml
	E-MEXP-2657-percentile-ranks.tsv	Tabular
	E-MEXP-2657.condensed-sdrf.tsv	Tabular

Items per page:

1 - 5 of 52

Similar Datasets

Transcription profiling by array of human stromal cells cultured with or without 3D BPH-1 prostate epithelial cells

Project description:BPH-1 prostate epithelial cells when cultured in Matrigel form 3D acini which closely recapitulate the tissue architecture of the prostate. The presence of primary stroma increases epithelial adhesions and causes changes in morphology. To identify the stromal signals which control actin/cadherin dynamics in epithelial cells we performed a microarray analysis on the stroma using Affymetrix U133 plus 2.0 arrays. Primary stroma from 7 different patients were cultured with (PSE) or without (PS) 3D BPH-1 epithelial acini to determine the gene expression changes within the stroma. The RNA from the Primary epithelia and stromal cultures were used at passages 1 or 1-3, respectively.

2010-06-09 | E-MEXP-2657 | biostudies-arrayexpress

Gene expression profiling of prostate epithelial cells in response to tissue contextual changes

Project description:To conduct comparative transcriptomic analyses on normal or malignant prostate epithelial cells in response to tissue contextual changes, we cultured immortalized prostate epithelial cells or prostate cancer cells as cell monolayers or three-dimensional organoids and profiled their transcriptomes in respective culture contexts. RWPE-1 (immortalized prostate epithelial cells) and LNCaP cells (prostate cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured within three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2) or acini or spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

2011-07-03 | E-GEOD-30304 | biostudies-arrayexpress

RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

Project description:FGF-2 is commonly used in culture media when growing mechenchymal stromal cells. Here, we cultured human MSCs from 3 donors with and without 50 ng/ml FGF-2 (Prepotech, human recombinant) in 3D PEG hydrogels, and analysed transcriptome changes by RNA sequencing.

2020-06-02 | E-MTAB-8510 | biostudies-arrayexpress

Affymetrix Stromal upregulation of lateral epithelial adhesions

Project description:Microarray analysis was used to identify genes that were differentially expressed when epithelial cells were grown in 3D Matrigel culture with stromal co-culture compared to without stroma.

2011-01-01 | E-MEXP-2990 | biostudies-arrayexpress

Operon Stromal upregulation of lateral epithelial adhesions

2011-01-01 | E-MEXP-2994 | biostudies-arrayexpress

Stromal-epithelial interaction via soluble factors in prostate carcinoma cell lines

Project description:Cell-cell communication is an important process in healthy tissue but also gains enhanced attention regarding pathological tissue. To date, the tumor microenvironment is gradually brought into focus when studying tumorigenesis. In the prostate gland, stromal and epithelial cells greatly interact to maintain homeostasis or tissue integrity. This study focuses on an indirect communication via soluble factors. For this approach, the prostate carcinoma cell line LNCaP and the stromal primary cells p21 were co-cultured without direct contact and RNA was isolated at defined time points (one, three and seven days). RNA sequencing finally revealed a time-depending differential expression profile.

2022-08-14 | GSE210988 | GEO

Primary prostate organoid transcriptomic profile in co-culture with primary prostate stroma

Project description:Organotypic in vitro culture is useful to model mammalian disease in numerous tissues. Normal epithelial differentiation and carcinogenesis both undergo in vivo regulation by stroma, but current culture methods exclude stroma. To mimic this in vivo environment, we developed and characterized a human 3D prostate organoid co-culture model that incorporates prostate stroma. Primary prostate stromal cells supported increased organoid formation and expressed growth factors and WNT-related genes involved in epithelial differentiation. Organoid branching occurred distal to physical contact with stromal cells, demonstrating non-random branching. Tumoroids derived from primary prostate cancer maintained differential expression of the prostate cancer marker AMACR only in the presence of stroma. Stroma-induced phenotypes were similar in all patients examined, yet maintained inter-patient heterogeneity in the degree of response. Addition of stroma to in vitro organoid culture recapitulated the in vivo microenvironment by inducing organization of benign organoids into branching structures and preserving prostate cancer phenotypes.

2018-05-30 | GSE115052 | 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

A soft stromal niche promotes hematopoietic stem cell maintenance and rejuvenation

Project description:Bulk RNA-seq data of 2D- vs. 3D-cultured human bone marrow stromal cells.

2024-09-15 | GSE184225 | GEO

Fibroblast-derived exosomal microRNA regulates NKX3-1 expression in androgen-sensitive, androgen receptor-dependent prostate cancer cells

Project description:The expression profiling of exosomal miRNAs produced by fibroblasts (human prostate stromal and three types of primary cultured prostate fibroblasts) revealed that certain fibroblast-produced exosomes may be involved in the suppression of oncogenic dedifferentiation in prostate cancer cells.

2024-05-10 | GSE232256 | GEO

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