Identification and validation of reference genes for gene expression studies in water buffalo

Abruzzo, 2005, Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data, BioTechniques, 38, 785, 10.2144/05385MT01 Andersen, 2004, Normalization of real-time quantitative reverse transcryptic-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets, Cancer Research, 64, 5245, 10.1158/0008-5472.CAN-04-0496 Aswal, 2007, Development of a competitive quantitative PCR strategy for evaluating the expression stability of 18s rRNA during in vitro maturation of buffalo (Bubalus bubalis) follicular oocytes, Reproduction in Domestic Animals, 42, 195, 10.1111/j.1439-0531.2006.00752.x Aswal, 2008, Expression stability of two reference genes (18s rRNA and G3PDH) during in vitro maturation of follicular oocytes in buffalo (Bubalus bubalis), Animal Reproduction Science, 103, 164, 10.1016/j.anireprosci.2007.04.012 Ayers, 2007, Expression stability of commonly used reference genes in canine articular connective tissues, BMC Veterinary Research, 3, 7, 10.1186/1746-6148-3-7 Bettegowda, 2006, Molecular Reproductive Development, 73, 267, 10.1002/mrd.20333 Bionaz, 2007, Identification of reference genes for quantitative real-time PCR in the bovine mammary gland during lactation cycle, Physiological Genomics, 29, 312, 10.1152/physiolgenomics.00223.2006 Bustin, 2002, Quantitation of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems, Journal of Molecular Endocrinology, 29, 23, 10.1677/jme.0.0290023 Czechowski, 2005, Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiology, 139, 5, 10.1104/pp.105.063743 De Ketelaere, 2006, Technical note: validation of internal control genes for gene expression analysis in bovine polymorphonuclear leukocytes, Journal of Dairy Science, 89, 4066, 10.3168/jds.S0022-0302(06)72450-X Ding, 2004, Quantitative analysis of nucleic acids-the last few years of progress, Journal of Biochemical Molecular Biology, 37, 1 Donaldson, 2005, Construction and validation of a bovine innate immune microarray, BMC Genomics, 6, 135, 10.1186/1471-2164-6-135 Faccioli, 2007, A combined strategy of “in silico” transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies, Plant Molecular Biology, 63, 679, 10.1007/s11103-006-9116-9 Feng, 2007, Extraction and quantitative analysis of stearoyl-coenzyme A desaturase mRNA from dairy cow milk somatic cells, Journal of Dairy Science, 90, 4128, 10.3168/jds.2006-830 Garcia-Crespo, 2005, Selection of ovine reference genes for normalisation by real-time RT-PCR; analysis of PrP gene expression and genetic susceptibility to scrapie, BMC Veterinary Research, 1, 3, 10.1186/1746-6148-1-3 Goossens, 2005, Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos, BMC Developmental Biology, 5, 27, 10.1186/1471-213X-5-27 Hocquette, 2002, Common practice in molecular biology may introduce statistical bias and misleading biological interpretation, Journal of Nutritional Biochemistry, 13, 370, 10.1016/S0955-2863(01)00216-9 Huggett, 2005, Real-time RT-PCR normalisation; strategies and considerations, Gene and Immunity, 6, 279, 10.1038/sj.gene.6364190 Khatib, 2006, The expression profile of the H19 gene in cattle, Mammalian Genome, 17, 991, 10.1007/s00335-006-0038-2 Kubista, 2006, The real-time polymerase chain reaction, Molecular Aspects of Medicine, 27, 95, 10.1016/j.mam.2005.12.007 Janovick-Guretzy, 2007, Reference gene expression in bovine liver is affected by physiological state, feed intake and dietary treatment, Journal of Dairy Science, 90, 2246, 10.3168/jds.2006-640 Jones, 1998, RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization, Analytical Biochemistry, 265, 368, 10.1006/abio.1998.2914 Lee, 2002, Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies, Genome Research, 12, 292, 10.1101/gr.217802 Lisowski, 2008, Evaluation of reference genes for studies of gene expression in the bovine liver, kidney, pituitary, and thyroid, Journal of Applied Genetics, 49, 367, 10.1007/BF03195635 Navani, 2002, A set of cattle microsatellite DNA markers for genome analysis of riverine buffalo (Bubalus bubalis), Animal Genetics, 33, 149, 10.1046/j.1365-2052.2002.00823.x Nicot, 2005, Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress, Journal of Experimental Botany, 56, 2907, 10.1093/jxb/eri285 Nolan, 2006, Current problems in quantitative real-time RT-PCR, Nature Protocols, 1, 1559, 10.1038/nprot.2006.236 Pfaffl, 2001, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acid Research, 29, e45, 10.1093/nar/29.9.e45 Pfaffl, 2001, Tissue-specific expression pattern of estrogen receptors (ER): quantification of ER alpha and ER beta mRNA with real-time RT-PCR, APMIS, 109, 345, 10.1034/j.1600-0463.2001.090503.x Radonic, 2004, Guidelines to reference gene selection for quantitative real-time PCR, Biochemical and Biophysical Research Communications, 313, 856, 10.1016/j.bbrc.2003.11.177 Ritz, 2000, Phylogenetic analysis of the tribe Bovini using microsatellites, Animal Genetics, 31, 178, 10.1046/j.1365-2052.2000.00621.x Robinson, 2007, Validation of candidate bovine reference genes for use with real-time PCR, Veterinary Immunology and Immunopathology, 115, 160, 10.1016/j.vetimm.2006.09.012 Schmittgen, 2000, Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR, Journal of Biochemical and Biophysical Methods, 46, 69, 10.1016/S0165-022X(00)00129-9 Schroeder, 2006, The RIN: an RNA integrity number for assigning integrity values to RNA measurements, BMC Molecular Biology, 7, 3, 10.1186/1471-2199-7-3 Stafuzza, 2007, Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3, Animal Genetics, 38, 406, 10.1111/j.1365-2052.2007.01612.x Vandesompele, 2002, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biology, 3, 10.1186/gb-2002-3-7-research0034 Warrington, 2000, Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes, Physiological Genomics, 2, 143, 10.1152/physiolgenomics.2000.2.3.143