Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 16
Release date: Nov 20 2014
Last update date: Jul 31 2017
Access: Public
Chemicals: Androgens
Dataset link Levator Ani Satellite Cells (LASCs) treated with Nonsteroidal Androgen Receptor Agonist (NARA)

Experimental Protocol


LASCs will be treated with one of the following conditions (N=4 for all groups): 1) 0.2% DMSO, 4 hours; 2) 10 nM NARA, 4 hours; 3) 0.2% DMSO, 48 hours; 4) 10nM NARA, 48 hours RNA was extracted using the PerfectPure RNA isolation kit (5 Prime, Gaithersburg, MD). Five micrograms of total RNA from each sample was labeled and hybridized to Affymetrix Rat Genome 230_2.0 microarrays according to Affymetrix protocols. Each microarray was washed and stained using an Affymetrix Fluidics Station 400 and scanned in an Affymetrix confocal GeneArray scanner. Affymetrix MAS5.0 software was used to scale data to a target intensity of 1500 and calculate transcript abundance (signal). Microarray signal intensities were generated by Affymetrix Expression Console using the MAS5 algorithm with targeted trimmed mean signal set to 1500. The gene chips were checked for quality control by their detection calls, chip pairwise correlation, and principal components analysis (PCA). Three chips (GSM1550754, GSM1550757, and GSM1550758) were identified as outliers and excluded from analysis for obvious low correlation with and deviating on PCA plots from the rest of the chips.

Repositories


GEO

GSE63489

ArrayExpress

E-GEOD-63489

BioProject

PRJNA268026

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Contact


James MacKrell
James G MacKrell