Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA seq of Primary MPM cell lines grown in 2D and 3D Nichoid

ABSTRACT: Our findings reveal that primary mesothelioma cells can be successfully propagated within nichoids, and the three-dimensional growth significantly influences the cells' integrity, impacting the mechanical stability of their structure

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ivan Ferrari

PROVIDER: E-MTAB-13749 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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.

2016-11-24 | GSE71259 | GEO

Effect of culture system on gene expression during traditional 2D culture and 3D culture of mouse mesothelioma cells

Project description:To investigate the differences between mesothelioma- organoid culture and 2D traditional culture, we established 7 mesothelioma lines and 3 normal mesothelial cells from model mouse. We then performed gene expression profiling analysis using data obtained from RNA-seq of 20 different cells.

2022-12-22 | GSE210310 | GEO

Effect of integrin alphaV on transcription in 2d or 3d

Project description:M21 or M21L cells were grown either in a 2-dimensional culture (on plastic) or in a 3-dimensional-collagen model.

2012-07-11 | GSE34219 | GEO

Expression profiling of 3D 2D MDCKII epithelial morphogenesis

Project description:Formation of epithelial tissues requires the generation of apical-basal polarity and the co-ordination of this polarity between neighboring cells to form a central lumen. MDCK cell line has proven to be a powerful model to study mammalian polarized epithelia in vitro. MDCK cells plated in extracellular matrix (ECM) form cysts, a spherical structure of polarized cells enclosing a central lumen which resembles epithelial tubular structures. The morphogenetic process requires drastic changes in cell architecture, which are regulated by change in gene expression. We used microarrays to identify genes up-regulated in lumen formation. The identification of up-regulated genes could lead us to characterize novel pathways needed for this process. MDCKII cells were plated in two different conditions: Cells cultured in confluence in plastic dishes, forming polarized monolayers (2D); or cells cultured in plastic dishes covered with Matrigel (ECM) forming three dimensional cysts (3D). Comparison of both transcriptomic profiles would lead us to identify up-regulated genes in the 3D condition, which would be good candidates to be key regulators of novel processes involved in lumen morphogenesis.

2011-09-30 | E-GEOD-32495 | biostudies-arrayexpress

Expression data from MSCs cultured on 3D and 2D matrixes

Project description:MSCs in vivo have a markedly different three-dimensioanal (3D) niche compared to the traditional two-dimensional (2D) culture in vitro. We used microarrays to detail the global difference of gene expression between MSCs cultured on 3D and 2D matrixes

2018-06-19 | GSE115947 | GEO

Gene expression profiling on 2D vs 3D iPSC colonies

Project description:In this study, we aimed to investigate the influence of the local mechanical cell niche on mechano-responsive signaling activities and germ layer specification by engineering a unique 3D semispherical colony of human-induced pluripotent stem cells (iPSCs). To achieve this, we utilized a combination of an electrospun nanofibrous substrate and PDMS microwells. Specifically, we compared the gene expression profiles of iPSCs cultured on a plastic plate with those cultured on a PCL nanofibrous substrate (19 kPa).

2023-06-13 | GSE234529 | GEO

Crosstalk with lung fibroblasts shapes the growth and therapeutic response of mesothelioma cells

Project description:Mesothelioma is an aggressive cancer of the mesothelial layer associated with an extensive fibrotic response. The latter is in large part mediated by cancer-associated fibroblasts which mediate tumour progression and poor prognosis. However, understanding of the crosstalk between cancer cells and fibroblasts in this disease is mostly lacking. Here, using co-cultures of patient-derived mesothelioma cell lines and lung fibroblasts, we demonstrate that fibroblast activation is a self-propagated process producing a fibrotic extracellular matrix (ECM) and triggering drug resistance in mesothelioma cells. Following characterisation of mesothelioma cells/fibroblasts signalling crosstalk, we identify several FDA-approved targeted therapies as far more potent than standard-of-care Cisplatin/Pemetrexed in ECM-embedded co-culture spheroid models. In particular, the SRC family kinase inhibitor, Saracatinib, extends overall survival well beyond standard-of-care in a mesothelioma genetically-engineered mouse model. In short, we lay the foundation for the rational design of novel therapeutic strategies targeting mesothelioma/fibroblast communication for the treatment of mesothelioma patients.

2024-01-26 | PXD040492 | Pride

The differences in miRNA expression with miRNA microarrays of two-dimensional (2D)- and three-dimensional (3D)-SNP cells

Project description:Canine mammary gland tumors can be used as predictive models for human breast cancer. There are several types of microRNAs common in human breast cancer and canine mammary gland tumors. The functions of microRNAs in canine mammary gland tumors are not well understood. In the present study, we compared the characterization of microRNA expression in two-dimensional and three-dimensional canine mammary gland tumor cell models. The expression of microRNA-210 in the three-dimensional-SNP cells was 10.19 times higher than that in the two-dimensional-SNP cells.

2022-07-07 | GSE203410 | GEO

3D Laparoscopy Versus 2D Laparoscopy

Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique. * To evaluate the visual overload in surgeons using 3D laparoscopic technique.

| 2220465 | ecrin-mdr-crc

Transcription profiling by array of A818-1 pancreatic cancer cells was grown either in 2D or 3D culture

Project description:The pancreatic cancer cell line A818-1 was grown either in 2D monolayers or in 3-dimensional “hollow spheres” as described in Lehnert et al. (1999), Ann N Y Acad Sci 880:83-93. Total RNA was extracted and analyzed from 3 independent experiments.

2015-02-27 | E-MTAB-3372 | biostudies-arrayexpress

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