Efficacy of RNA amplification is dependent on sequence characteristics: Implications for gene expression profiling using a cDNA microarray

Hoheisel, 2006, Microarray technology: beyond transcript profiling and genotype analysis, Nature, 7, 200 Xiao, 2005, Deoxyribonucleic acid microarray analysis of gene expression pattern in the arcuate nucleus/ventromedial nucleus of hypothalamus during lactation, Endocrinology, 146, 4391, 10.1210/en.2005-0561 Emmert-Buck, 1996, Laser capture microdissection, Science, 274, 998, 10.1126/science.274.5289.998 Bonner, 1997, Laser capture microdissection: molecular analysis of tissue, Science, 278, 1481, 10.1126/science.278.5342.1481 Ginsberg, 2004, Single-cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders, Neurochem. Res., 29, 1053, 10.1023/B:NERE.0000023593.77052.f7 Singh, 2005, Fluorescence-activated cell sorting of EGFP-labeled neural crest cells from murine embryonic craniofacial tissue, J. Biomed. Biotechnol., 3, 232, 10.1155/JBB.2005.232 Ji, 2004, A method for gene expression analysis by oligonucleotide arrays from minute biological materials, Anal. Biochem., 331, 329, 10.1016/j.ab.2004.03.039 Kurimoto, 2006, An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis, Nucleic Acids Res., 34, e42, 10.1093/nar/gkl050 Dulac, 1995, A novel family of genes encoding putative pheromone receptors in mammals, Cell, 83, 195, 10.1016/0092-8674(95)90161-2 Van Gelder, 1990, Amplified RNA synthesized from limited quantities of heterogeneous cDNA, Proc. Natl. Acad. Sci. USA, 87, 1663, 10.1073/pnas.87.5.1663 Nygaard, 2006, Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling, Nucleic Acids Res., 34, 996, 10.1093/nar/gkj499 Lockhart, 2000, Genomics, gene expression and DNA arrays, Nature, 405, 827, 10.1038/35015701 Gustincich, 2004, Gene discovery in genetically labeled single dopaminergic neurons of the retina, Proc. Natl. Acad. Sci. USA, 101, 5069, 10.1073/pnas.0400913101 Iscove, 2002, Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA, Nat. Biotechnol., 20, 940, 10.1038/nbt729 Wang, 2000, High-fidelity mRNA amplification for gene profiling, Nat. Biotechnol., 18, 457, 10.1038/74546 Baugh, 2001, Quantitative analysis of mRNA amplification by in vitro transcription, Nucleic Acids Res., 29, e29, 10.1093/nar/29.5.e29 Wang, 2005, RNA amplification for successful gene profiling analysis, J. Transl. Med., 5, 28, 10.1186/1479-5876-3-28 Upson, 2004, Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection, J. Cell. Physiol., 201, 366, 10.1002/jcp.20073 Ohara, 2005, cDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases, BioTechniques, 38, 451, 10.2144/05383RR01 Polacek, 2003, Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA, Physiol. Genomics, 13, 147, 10.1152/physiolgenomics.00173.2002 Thelen, 2004, cDNA microarray analysis with amplified RNA after isolation of intact cellular RNA from neoplastic and non-neoplastic prostate tissue separated by laser microdissections, Int. J. Oncol., 24, 1085 Nygaard, 2003, Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance, BMC Genomics, 4, 11, 10.1186/1471-2164-4-11 Park, 2004, Application of amplified RNA and evaluation of cRNA targets for spotted-oligonucleotide microarray, Biochem. Biophys. Res. Commun., 325, 1346, 10.1016/j.bbrc.2004.10.151 Schneider, 2004, Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments, BMC Genomics, 5, 29, 10.1186/1471-2164-5-29 Han, 2005, Novel multiple 5′-amino-modified primer for DNA microarrays, Genomics, 86, 252, 10.1016/j.ygeno.2005.04.009 Schindler, 2005, cRNA target preparation for microarrays: comparison of gene expression profiles generated with different amplification procedures, Anal. Biochem., 344, 92, 10.1016/j.ab.2005.06.006 Klur, 2004, Evaluation of procedures for amplification of small-size samples for hybridization on microarrrays, Genomics, 83, 508, 10.1016/j.ygeno.2003.09.005 Wadenbäck, 2005, Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays, BMC Genomics, 6, 61, 10.1186/1471-2164-6-61 van Haaften, 2006, Biologically relevant effects of mRNA amplification on gene expression profiles, BMC Bioinformatics, 7, 200, 10.1186/1471-2105-7-200 Renn, 2004, Biological meaningful expression profiling across species using heterologous hybridization to a cDNA microarray, BMC Genomics, 5, 42, 10.1186/1471-2164-5-42 Marko, 2005, A robust method for the amplification of RNA in the sense orientation, BMC Genomics, 6, 27, 10.1186/1471-2164-6-27 Dudoit, 2002, Statistical methods for identifying differentially expressed genes in replicated cDNA expression experiments, Stat. Sin., 12, 111 Whiteley, 2006, Proteomic patterns for cancer diagnosis—promise and challenges, Mol. BioSyst., 2, 358, 10.1039/B607260G Oleksiak, 2002, Variation in gene expression within and among natural populations, Nat. Genet., 32, 261, 10.1038/ng983 Arezi, 2003, Amplification efficiency of thermostable DNA polymerases, Anal. Biochem., 321, 226, 10.1016/S0003-2697(03)00465-2 Kunisawa, 1998, Comparison of synonymous codon distribution patterns of bacteriophage and host genomes, DNA Res., 5, 319, 10.1093/dnares/5.6.319 Bernardi, 2000, Isochores and the evolutionary genomics of vertebrates, Gene, 241, 3, 10.1016/S0378-1119(99)00485-0 Zhang, 2004, GC/AT-content spikes as genomic punctuation marks, Proc. Natl. Acad. Sci. USA, 101, 16855, 10.1073/pnas.0407821101 Nam, 2002, Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription, Proc. Natl. Acad. Sci. USA, 99, 6152, 10.1073/pnas.092140899 Hu, 2002, Obtaining reliable information from minute amounts of RNA using cDNA microarrays, BMC Genomics, 3, 16, 10.1186/1471-2164-3-16 Kenzelmann, 2004, High-accuracy amplification of nanogram total RNA amounts for gene profiling, Genomics, 83, 550, 10.1016/j.ygeno.2003.09.026 Smyth, 2005, Limma: linear models and empirical models for microarray data, 397 Smyth, 2003, Normalization of cDNA microarray data, Methods, 31, 265, 10.1016/S1046-2023(03)00155-5 Smyth, 2004, Linear models and empirical Bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 3, 10.2202/1544-6115.1027 Benson, 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res., 27, 573, 10.1093/nar/27.2.573 Hofacker, 1994, Fast folding and comparison of RNA secondary structures, Monatshefte f. Chemie, 125, 167, 10.1007/BF00818163 Perna, 1995, Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes, J. Mol. Ecol., 41, 353, 10.1007/BF01215182