A Common Reference for CDNA Microarray Hybridizations

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2002 Nov 1

PMID 12409475

Citations 18

Authors

Ellen Sterrenburg

Rolf Turk

Judith M Boer

GertJan B van Ommen

Johan T den Dunnen

Affiliations

Soon will be listed here.

Abstract

Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one experimental control sample, a pool of cell lines or a mix of all samples to be analyzed. We have developed an alternative common reference consisting of a mix of the products that are spotted on the array. Pooling part of the cDNA PCR products before they are printed and their subsequent amplification towards either sense or antisense cRNA provides an excellent common reference. Our results show that this reference yields a reproducible hybridization signal in 99.5% of the cDNA probes spotted on the array. Accordingly, a ratio can be calculated for every spot, and expression levels across different hybridizations can be compared. In dye-swap experiments this reference shows no significant ratio differences, with 95% of the spots within an interval of +/-0.2-fold change. The described method can be used in hybridizations with both amplified and non-amplified targets, is time saving and provides a constant batch of common reference that lasts for thousands of hybridizations.

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References

DeRisi J, Iyer V, Brown P . Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997; 278(5338):680-6. DOI: 10.1126/science.278.5338.680. View

Lennon G, Auffray C, Polymeropoulos M, Soares M . The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics. 1996; 33(1):151-2. DOI: 10.1006/geno.1996.0177. View

Luo L, Salunga R, Guo H, Bittner A, Joy K, Galindo J . Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med. 1999; 5(1):117-22. DOI: 10.1038/4806. View

Brown P, Botstein D . Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999; 21(1 Suppl):33-7. DOI: 10.1038/4462. View

Eisen M, Brown P . DNA arrays for analysis of gene expression. Methods Enzymol. 1999; 303:179-205. DOI: 10.1016/s0076-6879(99)03014-1. View

Perou C, Jeffrey S, van de Rijn M, Rees C, Eisen M, Ross D . Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999; 96(16):9212-7. PMC: 17759. DOI: 10.1073/pnas.96.16.9212. View

Alizadeh A, Eisen M, Davis R, Ma C, Lossos I, Rosenwald A . Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000; 403(6769):503-11. DOI: 10.1038/35000501. View

Ross D, Scherf U, Eisen M, Perou C, Rees C, Spellman P . Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000; 24(3):227-35. DOI: 10.1038/73432. View

Scherf U, Ross D, Waltham M, Smith L, Lee J, Tanabe L . A gene expression database for the molecular pharmacology of cancer. Nat Genet. 2000; 24(3):236-44. DOI: 10.1038/73439. View

10.

Alizadeh A, Eisen M, Davis R, Ma C, Sabet H, Tran T . The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol. 2001; 64:71-8. DOI: 10.1101/sqb.1999.64.71. View

11.

Yue H, Eastman P, Wang B, Minor J, Doctolero M, Nuttall R . An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 2001; 29(8):E41-1. PMC: 31325. DOI: 10.1093/nar/29.8.e41. View

12.

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R . Missing value estimation methods for DNA microarrays. Bioinformatics. 2001; 17(6):520-5. DOI: 10.1093/bioinformatics/17.6.520. View

13.

Tseng G, Oh M, Rohlin L, Liao J, Wong W . Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 2001; 29(12):2549-57. PMC: 55725. DOI: 10.1093/nar/29.12.2549. View

14.

Zehetner G, Pack M, Schafer K . Preparation and screening of high-density cDNA arrays with genomic clones. Methods Mol Biol. 2001; 175:169-88. DOI: 10.1385/1-59259-235-X:169. View

15.

Graf L, Heimfeld S, Torok-Storb B . Comparison of gene expression in CD34+ cells from bone marrow and G-CSF-mobilized peripheral blood by high-density oligonucleotide array analysis. Biol Blood Marrow Transplant. 2001; 7(9):486-94. DOI: 10.1053/bbmt.2001.v7.pm11669215. View

16.

J van t Veer L, Dai H, van de Vijver M, He Y, Hart A, Mao M . Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002; 415(6871):530-6. DOI: 10.1038/415530a. View

17.

Bergstrom D, Penn B, Strand A, Perry R, Rudnicki M, Tapscott S . Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression. Mol Cell. 2002; 9(3):587-600. DOI: 10.1016/s1097-2765(02)00481-1. View

18.

Dudley A, Aach J, Steffen M, Church G . Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A. 2002; 99(11):7554-9. PMC: 124281. DOI: 10.1073/pnas.112683499. View

19.

Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M . Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002; 18 Suppl 1:S96-104. DOI: 10.1093/bioinformatics/18.suppl_1.s96. View

20.

Van Gelder R, von Zastrow M, Yool A, Dement W, Barchas J, Eberwine J . Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A. 1990; 87(5):1663-7. PMC: 53542. DOI: 10.1073/pnas.87.5.1663. View