Microarray analysis of esophageal biopsies was performed by the CCHMC Gene Expression Microarray Core using the Affymetrix U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) as previously described.5 (link) In brief, RNA was isolated using the RNeasy kit (QIAGEN Incorporated, Germantown, MD) according to the manufacturer's protocol. For microarray analysis of BANCR or NSC shRNA–transduced cells, cells were treated with suboptimal doses of IL-13 (10 ng/mL) for 24 hours in triplicate. RNA quality assessment, library preparation, hybridization to the GeneChip® Human Gene 2.0 ST exon array (Affymetrix, Santa Clara, CA), and analyses were performed at the CCHMC Gene Expression Microarray Core. Data were normalized to the median of control/untreated samples, and statistical significance was determined using a Welch t-test with Benjamini-Hochberg false discovery rate (biopsies) or a 2-way ANOVA (BANCR shRNA) with a threshold of P < 0.05 and a 2.0- (biopsies) or 1.5-fold (BANCR shRNA) cut-off filter in GeneSpring® GX (Agilent Technologies Incorporated, Clara, CA).
Genechip human gene 2.0 st exon array
Manufactured by Thermo Fisher Scientific
Sourced in Canada
The GeneChip® Human Gene 2.0 ST exon array is a gene expression profiling tool designed for the analysis of exon-level expression. It contains probes targeting over 1 million exons across the human genome, enabling comprehensive coverage of transcript isoforms. The array provides a high-throughput platform for studying alternative splicing and gene-level expression.
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2 protocols using genechip human gene 2.0 st exon array
1
Microarray Analysis of Esophageal Biopsies
2
Microarray Analysis of Esophageal Biopsies
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Microarray analysis of esophageal biopsies was performed by the CCHMC Gene Expression Microarray Core using the Affymetrix U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) as previously described.5 (link) In brief, RNA was isolated using the RNeasy kit (QIAGEN Incorporated, Germantown, MD) according to the manufacturer's protocol. For microarray analysis of BANCR or NSC shRNA–transduced cells, cells were treated with suboptimal doses of IL-13 (10 ng/mL) for 24 hours in triplicate. RNA quality assessment, library preparation, hybridization to the GeneChip® Human Gene 2.0 ST exon array (Affymetrix, Santa Clara, CA), and analyses were performed at the CCHMC Gene Expression Microarray Core. Data were normalized to the median of control/untreated samples, and statistical significance was determined using a Welch t-test with Benjamini-Hochberg false discovery rate (biopsies) or a 2-way ANOVA (BANCR shRNA) with a threshold of P < 0.05 and a 2.0- (biopsies) or 1.5-fold (BANCR shRNA) cut-off filter in GeneSpring® GX (Agilent Technologies Incorporated, Clara, CA).
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