Dataset features


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Sep 3 2009
Last update date: Aug 23 2018
Access: Public
Diseases: Chemical and Drug Induced Liver Injury
Dataset link Gene expression from TCDD treated C57BL6/J and human Aryl hydrocarbon Receptor expressing primary mouse hepatocytes

Experimental Protocol

Isolated mouse hepatocytes from wild type and treated with 10nM TCDD for 6h were analyzed. 1 array per mouse (3 mice per treatment group) was used.GeneChip® Operating Software (Affymetrix) was utilized to preprocess CAB/CEL files generated from the 12 scanned microarrays which represented hepatocytes isolated from one mouse each. Data quality was initially assessed by checking the array image, B2 oligo performance, average background to noise ratios, poly-A controls, hybridization controls and the 3' to 5' probe-set ratios for control genes (e.g. ß-actin or GAPDH). Microarray data was normalized using Probe Logarithmic Intensity Error Approximation PLIER-MM algorithm (Affymetrix Expression Console™ Software 1.1). Normalized microarray data outputs from TCDD and control treated Ahrb/band AHRTtr hepatocytes were compared for differential expression using Significance Analysis of Microarrays (SAM, version 2.23A (Pan 2002; Tusher et al. 2001)) with 100 permutations, KNN-10.