Big results from small samples: evaluation of amplification protocols for gene expression profiling

Agnes Viale; Juan Li; Jay Tiesman; Susan Hester; Aldo Massimi; Chandi Griffin; George Grills; Greg Khitrov; Kathryn Lilley; Kevin Knudtson; Bill Ward; Karl Kornacker; Chin-Yi Chu; Herbert Auer; Andrew I Brooks

Big results from small samples: evaluation of amplification protocols for gene expression profiling

Journal article

Peer reviewed

Big results from small samples: evaluation of amplification protocols for gene expression profiling

Agnes Viale, Juan Li, Jay Tiesman, Susan Hester, Aldo Massimi, Chandi Griffin, George Grills, Greg Khitrov, Kathryn Lilley, Kevin Knudtson, …

Journal of biomolecular techniques, Vol.18(3), pp.150-161

07/2007

PMCID: PMC2062549

PMID: 17595311

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Abstract

Microarrays have revolutionized many areas of biology due to our technical ability to quantify tens of thousands of transcripts within a single experiment. However, there are still many areas that cannot benefit from this technology due to the amount of biological material needed for microarray analysis. In response to this demand, chemistries have been developed that boast the capability of generating targets from nanogram amounts of total RnA, reflecting minimal amounts of biological material, on the order of several hundred or thousand cells. Herein, we describe the evaluation of four chemistries for RnA amplification in terms of reproducibility, sensitivity, accuracy, and comparability to results from a single round of T7 amplification. No evidence for false-positive measurements of differential expression was observed. In contrast, clear differences between chemistries in sensitivity and accuracy were detected. PCR validation showed an interaction of probe sequence on the array and target labeling chemistry, resulting in a chemistry-dependent probe set sensitivity varying over an order of magnitude.

Cell Line, Tumor

Gene Expression Profiling - methods

Humans

Nucleic Acid Amplification Techniques - methods

Sample Size

Sensitivity and Specificity

Details

Title: Subtitle: Big results from small samples: evaluation of amplification protocols for gene expression profiling
Creators: Agnes Viale - Bionomics
Juan Li
Jay Tiesman
Susan Hester
Aldo Massimi
Chandi Griffin
George Grills
Greg Khitrov
Kathryn Lilley
Kevin Knudtson
Bill Ward
Karl Kornacker
Chin-Yi Chu
Herbert Auer
Andrew I Brooks - Environmental and Occupational Health Sciences Institute
Resource Type: Journal article
Publication Details: Journal of biomolecular techniques, Vol.18(3), pp.150-161
PMID: 17595311
PMCID: PMC2062549
ISSN: 1524-0215
eISSN: 1943-4731
Grant note: P30 ES005022 / NIEHS NIH HHS P30ES005022 / NIEHS NIH HHS
Language: English
Date published: 07/2007
Academic Unit: Iowa Institute of Human Genetics
Record Identifier: 9984627236102771

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