Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of neural stem cells in 3D hydrogels with different stiffness

ABSTRACT: We report a transcriptome sequencing to identify 3D hydrogel stiffness-dependent genes

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE193194 | GEO | 2022/01/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression profiling of neural stem cells in 3D hydrogels with different stiffness

Project description:Gene expression profiling of neural stem cells in 3D hydrogels with different stiffness

| PRJNA795362 | ENA

RNAseq analysis of mouse Eph4 mammary epithelial cells to determine their response to altered extracellular matrix stiffness

Project description:Almost all cells respond to the mechanical stiffness of their microenvironment through alter gene expression. Mammary epithelial cells respond to the mechanics of the extracellular matrix (ECM) in a way that can alter their behaviour and be pro-oncogenic. How increased ECM stiffness promotes transformation is unclear, but it can increase the incidence of DNA damage. This experiment was undertaken to identify changes in gene expression in non-tumorigenic mammary epithelial cells (murine Eph4) in response to different ECM stiffness. Epg4 cells were grown in either a soft or stiff 3D Matrigel-Alginate hydrogel, or on soft and stiff 2D polyacrylamide hydrogel. RNAseq was undertaken to identify gene expression changes associated with both stiffness and 2D vs. 3D culture conditions.

2025-10-22 | E-MTAB-15122 | biostudies-arrayexpress

Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [array]

Project description:Remodeling and increased stiffness of the extracellular matrix is a hallmark of solid cancers and contributes to tumor progression through increased proliferation, survival and migration. Mechanotransduction, the process in which cells sense and transduce mechanical signals, can result in transcriptional changes that in turn alter cellular behavior. In vitro culturing of MCF10ACA1a (CA1a) breast cancer cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic changes in morphology, indicating a stiffness dependent induction of a malignant phenotype. We used DNA microarray to characterize the transcriptome of CA1a cells on low (400 Pa) and high (5000 Pa) stiffness, corresponding to the stiffness of normal breast and breast cancer, respectively.

2023-03-13 | GSE205817 | GEO

Transcriptomic profiling of breast cancer cells on hydrogels with different stiffness [sequencing]

Project description:Remodeling and increased stiffness of the extracellular matrix is a hallmark of solid cancers and contributes to tumor progression through increased proliferation, survival and migration. Mechanotransduction, the process in which cells sense and transduce mechanical signals, can result in transcriptional changes that in turn alter cellular behavior. In vitro culturing of MCF10ACA1a (CA1a) breast cancer cells on polyacrylamide-based hydrogels of variable stiffness revealed drastic changes in morphology, indicating a stiffness dependent induction of a malignant phenotype. We used two different techniques, DNA microarray and RNA sequencing, to characterize the transcriptome of CA1a cells on low (500 Pa) and high (8000 Pa) stiffness, corresponding to the stiffness of normal breast and breast cancer, respectively.

2023-03-13 | GSE205816 | GEO

RNA-seq of 4T1 mouse breast cancer cells cultured on soft vs stiff polyacrylamide hydrogels for 24 hours

Project description:The tumour microenvironment is a critical element involved in tumour progression and responsiveness to therapies. Using functionalized tunable stiffness hydrogel, mimicking the mechanical properties of healthy and tumour tissues, we explore how the stiffness of the microenvironment can influence cancer cells by generating RNA-seq transcriptional profiles of 4T1 mouse breast cancer cells cultured on soft vs stiff polyacrylamide hydrogels for 24 hours.

2024-12-30 | E-MTAB-11487 | biostudies-arrayexpress

Influence of substrate stiffness on barrier function in an iPSC-derived in vitro blood-brain barrier model

Project description:Induced pluripotent stem cells were differentiated to brain microvascular endothelial-like (BMEC-like) cells and cultured on hydrogel substrates of varying stiffness. Cellular changes were measured by bulk transcriptome and proteome readouts.

2021-04-07 | E-MTAB-10336 | biostudies-arrayexpress

RGD-mediated biomimetic dynamic matrix stiffness signaling enable rapid 3D organoid formation

Project description:Stiffness of extracellular matrix (ECM) is crucial for regulating tissue morphogenesis and cellular behavior. The Arg-Gly-Asp (RGD) motif is a key integrin ligand. However, whether RGD regulates cellular function and tissue remodeling through mechanical stiffness-driven mechanical signaling remains unclear. Here, we develop an easily prepared, ECM-free RGD-functionalized carboxymethylcellulose (CMC) hydrogel. By modulating its mechanical strength, the synergistic effect between RGD-mediated integrin linking and matrix stiffness regulates the formation and expansion of a wide range of tissue-specific organoids through the mechanical transduction pathway of integrin β1/FAK/YAP. Finally, using this method, we develop an acral melanoma organoid model that simulates its development driven by mechanical force and provides a platform for drug screening. These results highlight that RGD-functionalized, stiffness-tunable hydrogel is an excellent biomimetic model for investigating mechanotransduction-driven cell development and disease progression, providing a low-cost strategy for future high-throughput drug screening using organoids.

2026-04-01 | PXD076446 |

RNA-seq of human skin fibroblasts from healthy and systemic sclerosis patients with varying matrix stiffness

Project description:This study explores how increased matrix stiffness alters fibroblast transcription and its impact on the lineage specification of fibroblast subpopulations in fibrotic skin. Fibroblasts from healthy and systemic sclerosis patients were cultured in a collagen I-based 3D system with varying matrix stiffness levels, and RNA sequencing was performed to identify stiffness-responsive genes.

2026-01-01 | E-MTAB-14804 | biostudies-arrayexpress

Cell Density Regulates Neural Stem Cells of Cellular Contact and Differentiation in 3D Hydrogel Culture System

Project description:Neural Stem Cells (NSCs) of biological behaviors are frequently regulated by the three-dimensional (3D) niches that they located in. The impact of cell density cue inside niche on cellular outcomes are usually underestimated and understudied. In this study, a facile NSCs of 3D culture system was developed using collagen self-assembled fibril hydrogel. We used RNA sequencing and molecular biology technologies to investigate the NSCs of cell contacts and differentiations in developed 3D hydrogel culture system with low (0.75 million/mL), medium (1.5 million/mL), and high (3 million/mL) cell packing density. Compared with low cell density system, cytoskeletal spreading, gap junction, and tight junction mediated cell contacts were significantly improved in high cell density culture. Moreover, high cell density increased NSCs differentiation into immature (Tuj1) neuron, while there is no discrepancy of NSCs differentiation into astrocytes in different cell densities of 3D culturing system. This study provides new understanding in the regulation of 3D cultured NSCs behaviors through niche of cell density cue.

2025-07-15 | GSE239619 | GEO

Mining the stiffness-sensitive transcriptome in human vascular smooth muscle cells identifies long non-coding RNA stiffness regulators

Project description:Vascular extracellular matrix (ECM) stiffening is a risk factor for aortic and coronary artery disease. How matrix stiffening regulates the transcriptome profile of human aortic (Ao) and coronary (Co) vascular smooth muscle cells (VSMCs) is not well understood. Furthermore, the role of long non-coding RNAs (lncRNAs) in the cellular response to stiffening has never been explored. This study characterizes the stiffness-sensitive transcriptome of human Ao and Co VSMCs and identify potentially key lncRNA regulators of stiffness-dependent VSMC functions. Ao and Co VSMCs were cultured on hydrogel substrates mimicking physiologic and pathologic ECM stiffness. Total RNA-seq was performed to compare the stiffness-sensitive transcriptome profiles of Ao and Co VSMCs.

2017-12-01 | GSE100081 | 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