Barbulovic-Nad I, Lucente M, Sun Y, Zhang M, Wheeler AR, Bussmann M (2006) Bio-microarray fabrication techniques—a review. Crit Rev Biotechnol 26:237–259
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res 39:D1005–D1010
Carvalho B, Bengtsson H, Speed TP, Irizarry RA (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8:485–499
[+]
Barbulovic-Nad I, Lucente M, Sun Y, Zhang M, Wheeler AR, Bussmann M (2006) Bio-microarray fabrication techniques—a review. Crit Rev Biotechnol 26:237–259
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res 39:D1005–D1010
Carvalho B, Bengtsson H, Speed TP, Irizarry RA (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8:485–499
Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, Wang S, Kurn N (2004) Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques 37:854–857
Dudoit S, Gentleman RC, Quackenbush J (2003) Open source software for the analysis of microarray data. Biotechniques, Suppl:45–51
Gonzalez-Ibeas D, Blanca J, Roig C, Gonzalez-To M, Pico B, Truniger V, Gomez P, Deleu W, Cano-Delgado A, Arus P, Nuez F, Garcia-Mas J, Puigdomenech P, Aranda M (2007) MELOGEN: an EST database for melon functional genomics. BMC Genomics 8:306
Gonzalez-Ibeas D, Cañizares J, Aranda MA (2011) Microarray analysis shows that recessive resistance to Watermelon mosaic virus in melon is associated with the induction of defense response genes. Mol Plant-Microbe Interact 25:107–118
Gubler U, Hoffman BJ (1983) A simple and very efficient method for generating cDNA libraries. Gene 25:263–269
Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320–326
Mascarell-Creus A, Cañizares J, Vilarrasa-Blasi J, Mora-García S, Blanca J, Gonzalez-Ibeas D, Saladié M, Roig C, Deleu W, Picó-Silvent B, López-Bigas N, Aranda MA, Garcia-Mas J, Nuez F, Puigdomènech P, Caño-Delgado AI (2009) An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.). BMC Genomics 10:467
Mathieu-Daudé F, Welsh J, Vogt T, McClelland M (1996) DNA rehybridization during PCR: the “Cot effect” and its consequences. Nucleic Acids Res 24:2080–2086
Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A (1999) Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res 27:1558–1560
Nygaard V, Løland A, Holden M, Langaas M, Rue H, Liu F, Myklebost O, Fodstad Ø, Hovig E, Smith-Sørensen B (2003) Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance. BMC Genomics 4:11
Okayama H, Berg P (1982) High-efficiency cloning of full-length cDNA. Mol Cell Biol 2:161–170
Page GP, Coulibaly I (2008) Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. Int J Plant Genomics 2008:147563
Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730
Puskás LG, Zvara A, Hackler L Jr, Van Hummelen P (2002) RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32:1330–1340
R Development Core Team. R (2010) A language and environment for statistical computing. Vienna, Austria
Raychaudhuri S, Stuart JM, Altman RB (2000) Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 2000:455–466
Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J (2006) TM4 microarray software suite. Methods Enzymol 411:134–193
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S (2002) A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 12:1935–1942
Soria-Guerra RE, Rosales-Mendoza S, Gasic K, Wisniewski ME, Band M, Korban SS (2011) Gene expression is highly regulated in early developing fruit of apple. Plant Mol Biol Rep 29:885–897
Stolf-Moreira R, Lemos EGM, Carareto-Alves L, Marcondes J, Pereira SS, Rolla AAP, Pereira RM, Neumaier N, Binneck E, Abdelnoor RV, Oliveira MCN, Marcelino FC, Farias JRB, Nepomuceno AL (2010) Transcriptional profiles of roots of different soybean genotypes subjected to drought stress. Plant Mol Biol Rep 29:19–34
Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87:1663–1667
Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM (2000) High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 18:457–459
Yang G, Zhou R, Tang T, Chen X, Ouyang J, He L, Li W, Chen S, Guo M, Li X, Shi S (2010) Gene expression profiles in response to salt stress in Hibiscus tiliaceus. Plant Mol Biol Rep 29:609–617
Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD (2001) Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30:892–897
[-]