Affymetrix Gene Expression Analysis

Aliquots (100 ng) of total RNA obtained from 3 animals per group on week 9 (cohort 1) and 4 animals per group on weeks 17 (cohort 2) and 22 (cohort 3) were individually converted to cRNA and labeled with a Gene ChIP® Poly-A RNA Control Kit, WT Amplification Kit, and Gene ChIP® WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Hybridization, washing, and staining were performed using Affymetrix® MoGene2.1 ST Array Strips and a GeneAtlas® Hybridization Wash and Stain Kit for WT Assay Strips (Affymetrix), according to the manufacturer’s protocols. After washing, MoGene2.1 Array Strips were analyzed using a GeneAtlas Imaging Station (Affymetrix). Data analyses were performed using Expression Console (Affymetrix) and Transcriptome Analysis Console (Affymetrix). The cut-off point: ≤−2 or ≥2 of a linear fold change and ANOVA P values were used as described in our previous studies^{45 (link),46 (link)}.

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Urmi J.F., Itoh H., Muramatsu-Kato K., Kohmura-Kobayashi Y., Hariya N., Jain D., Tamura N., Uchida T., Suzuki K., Ogawa Y., Shiraki N., Mochizuki K., Kubota T, & Kanayama N. (2019). Plasticity of histone modifications around Cidea and Cidec genes with secondary bile in the amelioration of developmentally-programmed hepatic steatosis. Scientific Reports, 9, 17100.

Publication 2019

Gene ChIP® Poly-A RNA Control Kit Gene ChIP® WT Terminal Labeling Kit MoGene2.1 ST Array Strips GeneAtlas Imaging Station Expression Console Transcriptome Analysis Console

Animals Anova Assay Crna Gene chip Hybridization Poly a rna Stain Transcriptome analysis

Corresponding Organization :

Other organizations : Hamamatsu University School of Medicine, Yamanashi Gakuin University, Kyushu University, Tokyo Institute of Technology, University of Yamanashi, Seitoku University

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Variable analysis

independent variables

Time (weeks 9, 17, and 22)

dependent variables

Gene expression profiles

control variables

Total RNA amount (100 ng) per sample
RNA conversion and labeling protocols (Gene Chip® Poly-A RNA Control Kit, WT Amplification Kit, and Gene Chip® WT Terminal Labeling Kit)
Hybridization, washing, and staining protocols (Affymetrix® MoGene2.1 ST Array Strips and GeneAtlas® Hybridization Wash and Stain Kit for WT Assay Strips)
Data analysis methods (Expression Console and Transcriptome Analysis Console)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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