Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 54
Release date: Mar 3 2015
Last update date: Nov 9 2017
Access: Public
Diseases: Lung Neoplasms, Neoplasms, Chronobiology Disorders
Dataset link Host Age is a Systemic Regulator of Gene Expression Impacting Cancer Progression

Experimental Protocol


For genome-wide expression profiling of tumor tissue, Mouse WG-6 BeadArray chips (Illumina, San Diego, CA) were used. Total RNA was amplified with the Ambion Illumina TotalPrep Amplification Kit (Ambion, Austin, TX) and labeled from all replicate biological samples for each condition. For tumor replicates, 20 tumor samples from adolescent, 10 from young adult, 10 from middle-aged, and 20 from old mice, were used. All replicate samples were run individually. Total RNA was isolated and purified using TRIzol (Invitrogen) and quantified using an Agilent Bioanalyzer. Samples were deemed suitable for amplification and hybridization if they had 28s/18s = 2:1, RIN >7. Total RNA of 500ng per sample was amplified using AmbionTotalPrep, and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C, the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. Data were corrected through normalization of the housekeeping genes, quantile normalized, then imported into MultiExperiment Viewer, MeV for analysis. Statistically significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction and false discovery rate (FDR) < 0.05 that resulted in a list of significant genes.

Repositories


GEO

GSE66414

ArrayExpress

E-GEOD-66414

BioProject

PRJNA276847

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Contact


Afshin Beheshti