Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human endothelial cell microRNA expression in high and low stiffness [sRNA-seq]

ABSTRACT: Purpose: Mechanical homeostasis is a crucial process for endothelial cell (EC) survival and functionality. Cells can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study, we observed change in microRNA levels linked with mechanical response. ECs were seeded for 48 hour on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then sRNA-seq was performed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110089 | GEO | 2020/02/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Human endothelial cell microRNA expression in high and low stiffness [RNA-seq]

Project description:Purpose: Mechanical homeostasis is a crucial process for endothelial cell (EC) survival and functionality. Cells can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study, we observed change in mRNA levels linked with mechanical response. ECs were seeded for 48 hour on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then RNA-seq was performed.

2020-02-02 | GSE110210 | GEO

Human Endothelial cell microRNA expression in high and low stiffness

Project description:Purpose: mechanical homeostasis is a crucial process for Humen dermal fibroblast cell (HDFs) survival and functionality. Cell can sense environmental change and modify the expression of extracellular matrix, focal adhesion and cytoskeleton protein to maintain the correct mechanical homeostasis. In this study we observed change in microRNA levels linked with mechanical response. HDFs were seeded for 48 our on PDMS 3 kPa and 30 kPa substrate coating with fibronectin to simulate "soft" and "stiff" substrate, then sRNA-seq was performed.

2019-03-31 | GSE123008 | GEO

Small extracellular vesicles promote stiffness-mediated metastasis

Project description:Tissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn aid cancer cell dissemination. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITGα2β1, ITGα6β4, ITGα6β1, CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) protein collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment.

2024-06-22 | PXD049019 | Pride

Modulation of Gene Expression by Substrate Stiffness via Regulation of Histone H2B Mono-ubiquitination

Project description:Mechanotransduction plays a critical role in regulating cell growth, proliferation, and metabolism. Cells respond to mechanical signals, which ultimately induces gene expression. However, the underlying mechanisms of this gene regulation remain largely unclear. In previous research, we discovered that the ubiquitin-conjugating enzymes UBE2A and UBE2B translocate between the cytoplasm and nucleus in a force-dependent manner. Additionally, we confirmed that UBE2A and UBE2B ubiquitinate histone H2B at lysine 120 (K120) when cells are cultured on a stiff substrate. In this study, we employed Chromatin Immunoprecipitation (ChIP) to investigate the distribution of H2B mono-ubiquitination in human skeletal muscle (hsSKM) cells cultured on substrates of varying stiffness—soft (0.2 kPa) and stiff (64 kPa).

2025-03-26 | GSE274425 | GEO

Substrate stiffness-dependent gene expression profile for cortical neurons

Project description:We undertook mRNA microarray and gene ontology analyses to screen out substrate stiffness-dependent genes. Total mRNA were extracted from E17 cortical neurons grown on soft or stiff substrates at 5 or 16 hr time points. We identified 114 differentially-expressed mRNA transcripts in cells grown on 0.1 kPa and 20 kPa gels at the 5 hr time-point. Among them, 66 were upregulated in 0.1 kPa gel cultures and the remainder were downregulated (compared to cells grown on stiffer substrates). The expressions of three endocytic genes (Cltc, Dab2, and Myo6) and four adhesion genes(Vcl, Robo2, Nrcam, and Cad11) were confirmed by QGP and smRNA FISH.

2018-01-08 | GSE102350 | 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

RNA-seq of primary rat macrophages cultured on substrates of defined stiffness

Project description:Cells interact with their mechanical environment and respond in consequence. Mechanical cues can have a wide range of influences on cell behaviour, ranging from guidance of differentiation and cell fate to immune activation. The impact of substrate stiffness on primary macrophages - a key player in innate immunity and inflammation - had not been previously studied. We prepared bone marrow-derived macrophage cultures from adult rat hematopoietic stem cells exposed to M-CSF, and cultured these on polyacrylamide substrates of controlled stiffness (ranging from 50 to 0.1 kPa shear modulus, covering the range found in physiological tissues) for 3 days. The RNA from these cells was then extracted and sequenced.

2023-04-15 | E-MTAB-7900 | biostudies-arrayexpress

Substrate elasticity does not impact on DNA methylation changes during differentiation of pluripotent stem cells.

Project description:Substrate elasticity may direct cell-fate decisions of stem cells. However, it is largely unclear how matrix stiffness impacts on differentiation of induced pluripotent stem cells (iPSCs) and if this is also reflected by epigenetic modifications. We have therefore cultured iPSCs on tissue culture plastic (TCP) and polydimethylsiloxane (PDMS) with different Young´s modulus (0.2 kPa, 16 kPa, or 64 kPa) to investigate the sequel on growth and differentiation towards endoderm, mesoderm, and ectoderm. Immunofluorescence and gene expression of canonical differentiation markers was hardly affected by the substrates. Notably, when we analyzed DNA methylation profiles of iPSCs or after three-lineage differentiation, we did not see any significant differences on the three different PDMS elasticities. Only when we compared DNA methylation profiles on PDMS-substrates versus TCP, we observed clear epigenetic differences, particularly upon mesodermal differentiation. Taken together, stiffness of PDMS-substrates did not impact on directed differentiation of iPSCs, whereas the moderate epigenetic differences on TCP might also be attributed to other chemical parameters.

2024-06-12 | GSE253190 | GEO

Surface stiffness, hydration, polydimethylsiloxane (PDMS), hyaluronic acid, biofilm and bacterial mobility, protein patterns.

Project description:By a global proteomic approach and phenotypic assays, we investigated the impact of surface stiffness on E. coli biofilm formation capacity. A global proteomic approach was used in order to identify the most abundant proteins for the comparison between E. coli adhesion in PDMS 9 kPa and 574kPa, (polydimethylsiloxane,), and between HA 44Pa and 2kPa (hyaluronic acid gels).

2023-03-11 | PXD035233 | Pride

Mechanical cues control mutant p53 stability through a Mevalonate/RhoA axis

Project description:To investigate the genes differentially expressed upon plating on top of matrixes with different stiffness, we compared the expression profiles of MDA-MB-231 breast cancer cells plated on a stiff substrate (plastic) with the same cells plated on a soft substrate (hydrogels 0.7 kPa). Keywords: expression profiling by array

2017-12-23 | GSE93529 | 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