Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole-genome expression data from normal FVB mouse lung tissue, transgenic cyclin E overexpressing (CEO) normal mouse lung tissue, and transgenic CEO lung adenocarcinomas

ABSTRACT: FVB mice were engineered to express wild-type human cyclin E under control of the human surfactant C promoter (CEO mice; Ma et al, PNAS 2007). These mice develop spontaneous lung tumors, which were shown to be adenocarcinoma by histological analysis. Here we compare whole-genome RNA expression levels between the tumors and normal lung of 4 CEO mice as well as 4 nontransgenic animals. RNA was isolated from the lungs of 4 FVB mice and adjacent normal and tumor tissue from 4 FVB transgenes harboring human surfactant protein C- driven wild-type human cyclin E, all 7-11 months in age. These samples were divided into 3 groups of four, and 12 independent hybridizations were performed for analysis with Affymetrix GeneChip Mouse 430 2.0 arrays.

ORGANISM(S): Mus musculus

SUBMITTER: Sarah Freemantle

PROVIDER: E-GEOD-45744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project 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.

Dataset Information

Whole-genome expression data from normal FVB mouse lung tissue, transgenic cyclin E overexpressing (CEO) normal mouse lung tissue, and transgenic CEO lung adenocarcinomas

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