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Transcriptome profiling of self-renewing hESCs and multipotent mesoderm progenitor cells as a function of substrate stiffness

ABSTRACT: We performed RNA-sequencing on human embryonic stem cell samples grown on soft (400Pa) and stiff (60kPa) hydrogels under self-renewal and differentiation conditions

ORGANISM(S): Homo sapiens

PROVIDER: GSE83584 | GEO | 2016/07/01

SECONDARY ACCESSION(S): PRJNA326429

REPOSITORIES: GEO

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Transcriptome profiling of self-renewing hESCs and multipotent mesoderm progenitor cells as a function of substrate stiffness

Project description:We performed RNA-sequencing on human embryonic stem cell samples grown on soft (400Pa) and stiff (60kPa) hydrogels under self-renewal and differentiation conditions Whole-transcriptome RNA sequencing in the conditions described

2016-07-01 | E-GEOD-83584 | biostudies-arrayexpress

Niche stiffness underlies the aging of CNS progenitor cells.

Project description:Next generation sequencing of OPCs grown on stiff and soft hydrogels

2019-07-06 | GSE133886 | GEO

RNA level differences between neurons in soft and stiff environments

Project description:Hippocampal rat neurons have been cultured on very soft (100 Pa) and stiff (10 kPa) hydrogels for 7 days. On DIV7, the RNA has been extracted and sequenced. The goal of this experiment is to understand why neurons mature more quickly on soft gels compared to stiff gels.

2023-12-01 | E-MTAB-11368 | biostudies-arrayexpress

Extracellular matrix (ECM) stiffness and collagen-1 (col-1) responsive genes in 3D cultured mammary epithelial cells

Project description:We report the expression profiles of MCF10A cells encapsulated in hydrogels of varying stiffness and composition. Cells were encapsulated for 7 days in either 1.) soft alginate and reconstituted basement membrane (rBM), 2.) stiff alginate and rBM, 3,) soft col-1 and rBM, or 4.) stiff col-1. We find global gene expression changes in response to enhanced ECM stiffness, independent of expression changes in response to col-1 exposure. These results provide a comprehensive study of the gene expression changes associated with increased ECM stiffness in addition to the gene expression changes associated with increased col-1 concentration in combination with, and independent of, ECM stiffness.

2019-03-25 | GSE102506 | GEO

Substrate stiffness effects on mRNA and lncRNA expression in mouse embryonic cardiomyocytes

Project description:Cardiomyocytes develop abnormal beating patterns and dedifferentiate on substrate with stiffness other than the physiological heart properties. This effect can be replicated in vitro with primary cardiomyocyte. To get a better idea of pathways involved and to identify new target genes, we aimed to compare mRNA and lncRNA of embryonic cardiomyocytes plated on either soft or stiff substrates

2020-04-18 | GSE109405 | 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

The impact of substrate stiffness on morphological, transcriptional and functional aspects in RPE [miRNA-Seq]

Project description:To investigate the influence of stiffness as a major Bruch's membrane characteristic on the RPE transcriptome and morphology. ARPE-19 cells were plated on soft or stiff polyacrylamide gels (PA gels) or standard tissue culture plastic (TCP). We then performed gene expression profiling analysis using data obtained from Next-generation sequencing of small RNAs of ARPE-19 cells cultured on 3 different biomechanical conditions.

2024-03-11 | GSE225641 | GEO

The impact of substrate stiffness on morphological, transcriptional and functional aspects in RPE [RNA-Seq]

2024-03-11 | GSE225640 | 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

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

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