Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 60
Release date: Feb 9 2018
Last update date: Jun 29 2018
Access: Public
Diseases: Pneumonia, Lipid
Computational protocol: affy, Pvclust, gplots, FactoMineR, ClueGO
Dataset link Expression data from normal weight/obese and sham/injured female C57BL/6J mice

Experimental Protocol


Muscle tissue from extensor iliotibialis anticus of normal weight and obese female mice, control and injury (n = 3). Harvesting time points were 1h, 6h, 24h, 3d and 8d to cover the early and middle stage regeneration process. Isolation of total RNA with subsequent microarray analysis performed with the Affymetrix system. 100 ng RNA per sample were used as described in the GeneChip® WT PLUS Reagent Kit from Affymetrix. Mouse Gene 1.0 ST Array GeneChip was used. Analysis of arrays was carried out with Affymetrix GeneChip Scanner 3000 and evaluated using Affymetrix Expression Console™. Evaluation of the CEL files was designed in R with RStudio. Briefly, injured versus control animals were normalized by RMA fit for time and diet, respectively. Pval function was used to determine p-values. Regulation of genes was first assessed without consideration for significance or expression levels to develop an unbiased time lapse heatmap. Significance level p ≤ 0.05 was introduced to screen for differentially expressed genes (DEG).

Repositories


GEO

GSE103726

BioProject

PRJNA406874

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