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Title: Low-dose, long-wave UV light does not affect gene expression of human mesenchymal stem cells      
dateReleased:
09-02-2015
description:
This experiment was conducted to test multiple hypotheses: 1) long-wave 365 nm UV light exposure at low fluences does not alter gene expression of hMSC, 2) presence of radical species during polymerization causes DNA damage in hMSC, 3) 3D encapsulation of hMSC causes changes in gene expression of hMSC compared with traditional 2D culture, 4) Differencesin 3D hydrogel networks induce gene expression changes in hMSC The first publication derived from this data set concerns UV exposure and reactive radical species. Light is a non-invasive tool that is widely used in a range of biomedical applications. Techniques such as photopolymerization, photodegradation and photouncaging can be used to alter the chemical and physical properties of biomaterials in the presence of live cells. Long-wave UV light is an easily accessible and commonly used wavelength. Although exposure to low doses of long-wave UV light is generally accepted as biocompatible, most studies only investigate cell viability, ignoring other possible non-toxic effects. Since light exposure could potentially induce phenotypic changes (i.e. if damage repair mechanisms are activated), we examined changes in gene expression of human mesenchymal stem cells exposed to light under various 2D and 3D culture conditions. While exposure to long-wave UV light did not induce any significant changes in gene expression regardless of culture conditions, significant changes were observed due to scaffold fabrication chemistry and between cells plated in 2D versus 3D scaffolds. In total, 24 samples were analyzed. Three different culture conditions were created: 2D(plated), 3DR (encapsulated, radical polymerization), and 3DC (encapsulated, conjugate addition). Each culture condition was further subjected to UV radiation or no UV radiation, for 6 total experimental groups. Each experimental group was performed in triplicate. The 2D experimental groups, with and without UV, were additionally performed twice, once simultaneously with the 3DR samples, and once simultaneously with the 3DC samples. 3DR: encapsulated cells using radical polymerization (APS/TEMED) in a poly(ethylene glycol) (MW=4,000 g/mol) hydrogel in PBS. 3DC: encapsulated cells using conjugate addition with a four-arm PEG-Thiol (pentaerythritol tetrakis(3-mercaptopropionate) (PETMP) ) as the cross-linker in PBS.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-58093
refinement:
raw
alternateIdentifiers:
58093
keywords:
functional genomics
dateModified:
09-05-2015
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-AFFY-44
name:
Affymetrix GeneChip Human Genome U133 Plus 2.0 [HG-U133_Plus_2]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58093/E-GEOD-58093.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58093/E-GEOD-58093.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58093
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress