Transcriptomics

Dataset Information

10

Transcription profiling of human (36) gastrointestinal tumors and normal tissues for house keeping gene analysis


ABSTRACT: Accurate and reproducible quantitation of target genes depends on correct normalization. Historically, genes with variable tissue transcription e.g. GAPDH, have been used as normalization factors which is problematic, particularly in clinical samples which often are derived from different tissue sources. Using a large-scale gene database (GeneChip (Affymetrix U133A) dataset of 36 gastrointestinal tumors and normal tissues), we identified 8 candidate reference genes that were highly expressed with low variability and established expression levels by real-time RT-PCR in an independent set of GI tissue samples (n=42). Experiment Overall Design: (GeneChip (Affymetrix U133A) dataset of 36 gastrointestinal tumors and Affymetrix protocol: http://keck.med.yale.edu/affymetrix/analysis.htm

ORGANISM(S): Homo sapiens  

SUBMITTER: Mark Kidd  

PROVIDER: E-GEOD-6272 | ArrayExpress | 2008-06-14

SECONDARY ACCESSION(S): GSE6272PRJNA99659

REPOSITORIES: GEO, ArrayExpress

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Publications

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR.

Kidd Mark M   Nadler Boaz B   Mane Shrikant S   Eick Geeta G   Malfertheiner Maximillian M   Champaneria Manish M   Pfragner Roswitha R   Modlin Irvin I  

Physiological genomics 20070424 3


Accurate quantitation of target genes depends on correct normalization. Use of genes with variable tissue transcription (GAPDH) is problematic, particularly in clinical samples, which are derived from different tissue sources. Using a large-scale gene database (Affymetrix U133A) data set of 36 gastrointestinal (GI) tumors and normal tissues, we identified 8 candidate reference genes and established expression levels by real-time RT-PCR in an independent data set (n = 42). A geometric averaging m  ...[more]

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