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

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

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

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

RNA-seq of CAF05s grown on different substrates

Project description:Almost all solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate the stiffening. While the biochemical crosstalk between CAFs and cancer cells have been widely investigated, it is yet not clear whether CAFs in stiffer TME promote metastatic progression, and if so, how. To address this question, here we explore the role of mechanical stiffness and cell traction force in regulating human colorectal CAF (CAF05 cell line) gene expressions that are relevant to metastatic progression. We cultured CAFs on 2D polyacrylamide hydrogels with increasing elastic modulus (E) of 1, 10 and 40 kPa, and quantified corresponding cell spreading area and cytoskeletal force. We performed genome-wide transcriptome analyses in these cells to identify differentially expressed genes on 40 KPa compared to those on 1 kPa substrate. The latter represents normal tissue stiffness of colon.

2023-04-18 | GSE229742 | GEO

RNA-seq of CAFs grown on different substrates

2022-06-15 | GSE205937 | GEO

Next-generation sequencing facilitates quantitative analysis of rat BMSCs in soft or stiff SA hydrogel

Project description:Purpose: To identify genes and the molecular pathways involved in the MSCs response to extracellular matrix stiffness, we performed RNA-sequencing of MSCs which cultured in soft (2 kPa) and stiff (18 kPa) SA hydrogels. Methods: mRNA profiles of MSCs cultured in soft (2 kPa) and stiff (18 kPa) SA hydrogel for 48 h were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000. Results: Using an optimized data analysis workflow, we identified 33950 transcripts in MSCs with BWA workflow. Conclusions: Our results present the detailed analysis of MSCs transcriptomes cultured in soft (2 kPa) and stiff (18 kPa) matrix, and found that matrix stiffness dominated multiple mRNA pathways in MSCs.

2021-08-06 | GSE181512 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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