Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level

Genome Biology

Volumn 7, Issue 3, 2006, Pages

  Subkhankulova, Tatiana ^a   Livesey, Frederick J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; PRIMER DNA; VIRUS PROTEIN;

ANIMAL CELL; ARTICLE; CELL ASSAY; CELL TYPE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; FALSE POSITIVE RESULT; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; IN VITRO STUDY; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MOUSE; NEURAL STEM CELL; NONHUMAN; POLYMERASE CHAIN REACTION; RELIABILITY; RNA ANALYSIS; TERMINAL OLIGOPYRIMIDINE TRACT; ANIMAL; CELL LINE; CELL STRAIN 3T3; COMPARATIVE STUDY; DNA MICROARRAY; FEMALE; GENETICS; METHODOLOGY; OVARY; REPRODUCIBILITY; STANDARD;

EUKARYOTA;

3T3 CELLS; ANIMALS; CELL LINE; DNA PRIMERS; DNA-DIRECTED RNA POLYMERASES; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 33745025941     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-3-r18     Document Type: Article

References (35)

1. Player A, Barrett JC, Kawasaki ES: Laser capture microdissection, microarrays and the precise definition of a cancer cell. Expert Rev Mol Diagn 2004, 4:831-840.
2. Kamme F, Salunga R, Yu J, Tran DT, Zhu J, Luo L, Bittner A, Guo HQ, Miller N, Wan J, Erlander M: Single-cell microarray analysis in hippocampus CAI: demonstration and validation of cellular heterogeneity. J Neurosci 2003, 23:3607-3615.
3. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270:484-487.
4. Livesey FJ: Strategies for microarray analysis of limiting amounts of RNA. Brief Funct Genomic Proteomic 2003, 2:31-36.
5. Eberwine J. Yeh H, Miyashiro K, Cao Y, Nair S. Finnell R, Zettel M, Coleman P: Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 1992, 89:3010-3014.
6. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH: Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 1990, 87:1663-1667.
7. Brady G, Iscove NN: Construction of cDNA libraries from single cells. Methods Enzymol 1993, 225:611-623.
8. Brady G. Billa F, Knox J, Hoang T, Kirsh IR, Voura EB, Hawley R, Cumming R, Buchwald M, Siminovitch K: Analysis of gene expression in a complex differentiation hierarchy by global amplification of cDNA from single cells. Curr Biol 1995, 5:909-922.
9. Dixon AK, Richardson PJ, Lee K. Carter NP, Freeman TC: Expression profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Res 1998, 26:4426-4431.
10. Liu CL, Schreiber SL, Bernstein BE: Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 2003, 4:19.
11. Patel OV, Suchyta SP, Sipkovsky SS, Yao, J, Ireland JJ, Coussens PM, Smith GW: Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Vet Immunol Immunopothol 2005, 105:331-342.
12. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed Al, White J. Li J, et al.: Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 2002, 3:research0062.
13. Zhao H, Hastie T, Whitfield ML, Borresen-Dale AL, Jeffrey SS: Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics 2002, 3:31.
14. Jenson SD, Robetorye RS, Bohling SD, Schumacher JA, Morgan JW, Lim MS, Elenitoba-Johnson KS: Validation of cDNA microarray gene expression data obtained from linearly amplified RNA. Mol Pothol 2003, 56:307-312.
15. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM: High-fidelity mRNA amplification for gene profiling. Not Biotechnol 2000, 18:457-459.
16. Goff LA, Bowers J. Schwalm J, Howerton K, Getts RC, Hart RP: Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genomics 2004, 5:76.
17. Spiess AN, Mueller N, Ivell R: Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 2003, 4:44.
18. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N: Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 2002, 20:940-943.
19. Matz M. Shagin D. Bogdanova E, Britanova O, Lukyanov S. Diatchenko L. Chenchik A: Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res 1999, 27:1558-1560,
20. Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD: Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 2001, 30:892-897.
21. Vernon SD, Unger ER, Rajeevan M, Dimulescu IM, Nisenbaum R, Campbell CE: Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays. J Mol Diagn 2000, 2:124-127.
22. Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA: Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003, 31:e142.
23. Livesey FJ, Furukawa T, Steffen MA, Church GM, Cepko CL: Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 2000, 10:301-310.
24. Puskas LG, Zvara A, Hackler L Jr, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32:1330-1334, 1336, 1338, 1340.
25. Chenchik A, Zhu YY, Diatchenko, L, Li R, Hill J, Siebert PD: Generation and use of high-quality cDNA form small amounts of total RNA by SMART PCR. In Gene Cloning and Analysis by RT-PCR Edited by: Siebert P, Larrick J, Natick MA. USA: Biotechniques Books; 1998:305-319.
26. Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat Sinica 2002, 12:111-139.
27. Bland JM, Altman DG: Measuring agreement in method comparison studies. Stat Methods Med Res 1999, 8:135-160.
28. Wilson CL, Pepper SD, Hey Y, Miller CJ: Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques 2004, 36:498-506.
29. Nygaard V, Loland A, Holden M, Langaas M, Rue H, Liu F, Myklebost O, Fodstad O, Hovig E, Smith-Sorensen B: Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance. BMC Genomics 2003, 4:11.
30. Richter A, Schwager C, Hentze S, Ansorge W, Hentze MW, Muckenthaler M: Comparison of fluorescent tag DNA labeling methods used for expression analysis by DNA microarrays. Biotechniques 2002, 33:620-628, 630.
31. t Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT: Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res 2003, 31:e20.
32. Ihaka R, Gentleman R: R: A language for data analysis and graphics. J Comput Graph Stat 1996, 5:299-314.
33. Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. Springer, New York:397-420.
34. Lönnstedt I, Speed T: Replicated microarray data. Stat Sinica 2002, 12:31-46.
35. Jenssen TK, Langaas M, Kuo WP, Smith-Sorensen B, Myklebost O, Hovig E: Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 2002, 30:3235-3244.