Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis

Plant Physiology

Volumn 139, Issue 1, 2005, Pages 5-17

  Czechowski, Tomasz ^a   Stitt, Mark ^a   Altmann, Thomas ^a   Udvardi, Michael K ^a   Scheible, Wolf Rüdiger ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; PLANTS (BOTANY); RNA;

ARABIDOPSIS; ENVIRONMENTAL STIMULI; GENE TRANSCRIPTS; HYBRIDIZATION; POLYMERASE CHAIN REACTION (PCR);

GENES;

ENZYMES; GENES; NUCLEIC ACIDS; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; MESSENGER RNA; PLANT RNA;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; METHODOLOGY; PLANT; PLANT LEAF; PLANT ROOT; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STANDARD;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT LEAVES; PLANT ROOTS; PLANT SHOOTS; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; RNA, PLANT; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION, GENETIC;

EID: 32644481938     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.105.063743     Document Type: Review

References (32)

1. Altmann T, Weigel D, Nover L (2004) AtGenExpress-Ein multinational koordiniertes Programm zur Erforschung des Arabidopsis Transkriptoms. GenomXpress 3: 13-14
2. Andersen CL, Jensen JK, Orntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250
3. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19: 185-193
4. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4: 14
5. Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR RT-PCR: trends and problems. J Mol Endocrinol 29: 23-29
6. Charrier B, Champion A, Henry Y, Kreis M (2002) Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction. Plant Physiol 130: 577-590
7. Coker JS, Davies E (2003) Selection of candidate housekeeping controls in tomato plants using EST data. Biotechniques 35: 740-743
8. Czechowski T, Bari RP, Stitt M, Scheible W-R, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38: 366-379
9. Dheda K, Huggett JT, Bustin SA, Johnson MA, Rook G, Zumla A (2004) Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37: 112-119
10. Gachon C, Mingam A, Charrier B (2004) Real-time PCR: what relevance to plant studies? J Exp Bot 55: 1445-1454
11. Goidin D, Mamessier A, Staquet M-J, Schmitt D, Berthier-Vergnes O (2001) Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and β-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and non-invasive human melanoma cell subpopulations. Anal Biochem 295: 17-21
12. Holland MJ (2002) Transcript abundance in yeast varies over six orders of magnitude. J Biol Chem 277: 14363-14366
13. Kim B-R, Nam H-Y, Kim S-U, Kim S-I, Chang Y-J (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25: 1869-1872
14. Lee PD, Sladek R, Greenwood CMT, Hudson TJ (2001) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12: 292-297
15. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, et al (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16: 2089-2103
16. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol Plant 15: 473-497
17. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45
18. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett 26: 509-515
19. Radonić A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A (2004) Guideline for reference gene selection for quantitative real-time PCR. Biochem Biophys Commun 313: 856-862
20. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 13: 62-66
21. Redman JC, Haas BJ, Tanimoto G, Town CD (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 38: 545-561
22. Sanderfoot AA, Raikhel NV (2002) The secretory system of Arabidopsis. In CR Somerville, EM Meyerowitz, eds, The Arabidopsis Book. American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0098, http://www.aspb.org/ publications/arabidopsis/
23. Scheible W-R, Morcuende R, Czechowski T, Fritz C, Osuna D, Palacios-Rojas N, Schindelasch D, Thimm O, Udvardi MK, Stitt M (2004) Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol 136: 2433-2499
24. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann J (2005) A gene expression map of Arabidopsis development. Nat Genet 37: 501-506
25. Shen L, Gong J, Caldo RA, Nettleton D, Cook D, Wise RP, Dickerson JA (2005) BarleyBase-an expression profiling database for plant genomics. Nucleic Acids Res 33: D614-D618
26. Smalle J, Vierstra RD (2004) The ubiquitin 26s proteasome proteolytic pathway Annu Rev Plant Biol 55: 555-590
27. Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004)CSB.DB: a comprehensive systems-biology database. Bioinformatics 20: 3647-3651
28. Suzuki T, Higgins PJ, Crawford DR (2000) Control selection for RNA quantitation. Biotechniques 29: 332-337
29. Thellin O, Zorzi W, Lakaye B. De Borman B, Coumans B, Henne G, Grisar T, Igout A, Heinen E (1999) Housekeeping genes as internal standards: use and limits. J Biotechnol 75: 197-200
30. Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939
31. Vandesompele J, De Preter K, Pattyn F, Puppe B. Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Bid 37: RESEARCH0034 Wan C-Y, Wilkins TA (1994) A modified hot-borate method significantly enhances the yield of high-quality RNA from cotton Gossypium hirsutum L. Anal Biochem 223: 7-12
32. Zimmermann P, Hirsch- Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136: 2621-2632