Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

BMC Molecular Biology

Volumn 9, Issue , 2008, Pages

  Pérez, Raquel ^a   Tupac Yupanqui, Isabel ^a   Dunner, Susana ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 MICROGLOBULIN; BETA ACTIN; CANCER SUSCEPTIBILITY CANDIDATE 3; ELONGATION FACTOR 1ALPHA; EUKARYOTIC TRANSLATION ELONGATION FACTOR 1ALPHA 2; GENE PRODUCT; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; MESSENGER RNA; PORPHOBILINOGEN DEAMINASE; RNA 18S; RNA POLYMERASE II; SPLICING FACTOR 3 SUBUNIT 1; UBIQUITIN C; UNCLASSIFIED DRUG;

ALGORITHM; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; COW; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; GENETIC STABILITY; HOUSEKEEPING GENE; MUSCLE TISSUE; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ANIMAL; BIOSYNTHESIS; CATTLE; GENE DOSAGE; GENETICS; METABOLISM; REFERENCE VALUE; SKELETAL MUSCLE;

BOVINAE;

ALGORITHMS; ANIMALS; CATTLE; GENE DOSAGE; GENE EXPRESSION PROFILING; MUSCLE, SKELETAL; REFERENCE VALUES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 53349108354     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-79     Document Type: Article

References (43)

1. Puntschart A Wey E Jostarndt K Vogt M Wittwer M Widmer HR Hoppeler H Billeter R Expression of fos and jun genes in human skeletal muscle after exercise Am J Physiol 1998, 274(1 Pt 1):C129-C137. 9458721
2. Pattison JS Folk LC Madsen RW Childs TE Spangenburg EE Booth FW Expression profiling identifies dysregulation of myosin heavy chains IIb and IIx during limb immobilization in the soleus muscles of old rats J Physiol 2003, 553(Pt 2):357-68. 2343579 12963800 10.1113/ jphysiol.2003.047233
3. Bernard C Cassar-Malek I Le Cunff M Dubroeucq H Renand G Hocquette JF New indicators of beef sensory quality revealed by expression of specific genes J Agric Food Chem 2007, 55(13):5229-37. 10.1021/jf063372l 17547415
4. Pal NR Aguan K Sharma A Amari S Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering BMC Bioinformatics 2007, 8:5. 1770936 17207284 10.1186/1471-2105-8-5
5. Heid CA Stevens J Livak KJ Williams PM Real time quantitative PCR Genome Res 1996, 6(10):986-94. 10.1101/gr.6.10.986 8908518
6. Bustin SA Benes V Nolan T Pfaffl MW Quantitative real-time RT-PCR - a perspective J Mol Endocrinol 2005, 34(3):597-601. Review. 10.1677/ jme.1.01755 15956331
7. Imbeaud S Graudens E Boulanger V Barlet X Zaborski P Eveno E Mueller O Schroeder A Auffray C Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces Nucleic Acids Res 2005, 33:e56. 1072807 15800207 10.1093/nar/ gni054
8. Bustin SA Tenth annual nucleic acid-based technologies: Time to stop and think Expert Rev Mol Diagn 2002, 2(5):405-8. 10.1586/14737159.2.5.405 12271812
9. Lekanne Deprez RH Fijnvandraat AC Ruijter JM Moorman AFM Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions Anal Biochem 2002, 307:63-69. 10.1016/S0003-2697(02)00021-0 12137780
10. Stahlberg A Hakansson J Xian X Semb H Kubista M Properties of the reverse transcription reaction in mRNA quantification Clin Chem 2004, 50(3):509-15. 10.1373/clinchem.2003.026161 14726469
11. Huggett J Dheda K Bustin S Zumla A Real-time RT-PCR normalisation; strategies and considerations Genes Immun 2005, 6:279-284. 10.1038/ sj.gene.6364190 15815687
12. Bustin SA Nolan T Pitfalls of Quantitative Real-Time Reverse-Transcription Polymerase Chain Reaction J Biomol Tech 2004, 15:155-166. 2291693 15331581
13. Dheda K Huggett JF Bustin SA Johnson MA Rook G Zumla A Validation of housekeeping genes for normalizing RNA expression in real-time PCR Biotechniques 2004, 37:112-119. 15283208
14. Schmittgen TD Zakrajsek BA Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR J Biochem Biophys Methods 2000, 20;46(1-2):69-81. 10.1016/ S0165-022X(00)00129-9
15. Tricarico C Pinzani P Bianchi S Paglierani M Distante V Pazzagli M Bustin SA Orlando C Quantitative real-time reverse transcription polymerase chain reaction: Normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies Anal Biochem 2002, 309(2):293-300. 10.1016/S0003-2697(02)00311-1 12413463
16. Vandesompele J De Preter K Pattyn F Poppe B Van Roy N De Paepe A Speleman F Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Genome Biology 2002, 3:0034.1-0034.11. 10.1186/gb-2002-3-7-research0034
17. Pfaffl MW Tichopad A Prgomet C Neuvians TP Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper- Excel-based tool using pair-wise correlations Biotechnology Letters 2004, 26:509-515. 10.1023/ B:BILE.0000019559.84305.47 15127793
18. Andersen CL Jensen JL Orntoft TF 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 2004, 64:5245-5250. 10.1158/ 0008-5472.CAN-04-0496 15289330
19. Murphy RM Watt KK Cameron-Smith D Gibbons CJ Snow RJ Effects of creatine supplementation on housekeeping genes in human skeletal muscle using real-time RT-PCR Physiol Genomics 2003, 12(2):163-74. 12419855
20. Timmons JA Jansson E Fischer H Gustafsson T Greenhaff PL Ridden J Rachman J Sundberg CJ Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans BMC Biol 2005, 3:19. 1224855 16138928 10.1186/1741-7007-3-19
21. de Jonge HJ Fehrmann RS de Bont ES Hofstra RM Gerbens F Kamps WA de Vries EG Zee van der AG te Meerman GJ ter Elst A Evidence based selection of housekeeping genes PLoS ONE 2, 9:e898. 2007 Sep 19 1976390 17878933 10.1371/journal.pone.0000898
22. Razeghi P Young ME Abbasi S Taegtmeyer H Hypoxia in vivo decreases peroxisome proliferator-activated receptor alpha-regulated gene expression in rat heart Biochem Biophys Res Commun 287, 1-5. 10 2001 Sep 14 10.1006/bbrc.2001.5541 11549245
23. Marcell TJ Harman SM Urban RJ Metz DD Rodgers BD Blackman MR Comparison of GH, IGF-I, and testosterone with mRNA of receptors and myostatin in skeletal muscle in older men Am J Physiol Endocrinol Metab 2001, 281(6):E1159-64. 11701429
24. Mahoney DJ Parise G Melov S Safdar A Tarnopolsky MA Analysis of global mRNA expression in human skeletal muscle during recovery from endurance exercise FASEB J 2005, 19(11):1498-500. 15985525
25. Birot OJ Koulmann N Peinnequin A Bigard XA Exercise induced expression of vascular endothelial growth factor mRNA in rat skeletal muscle is dependent on fibre type J Physiol 2003, 552:213-221. 2343332 12860922 10.1113/jphysiol.2003.043026
26. Mahoney DJ Carey K Fu MH Snow R Cameron-Smith D Parise G Tarnopolsky MA Real-time RT-PCR analysis of housekeeping genes in human skeletal muscle following acute exercise Physiol Genomics 2004, 18:226-231. 10.1152/ physiolgenomics.00067.2004 15161965
27. Jemiolo B Trappe S Single muscle fiber gene expression in human skeletal muscle: Validation of internal control with exercise Biochem Biophys Res Commun 2004, 320:1043-1050. 10.1016/j.bbrc.2004.05.223 15240153
28. Erkens T Van Poucke M Vandesompele J Goossens K Van Zeveren A Peelman LJ Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A BMC Biotechnol 2006, 6:41. 1609116 17026777 10.1186/1472-6750-6-41
29. Nygard AB Jørgensen CB Cirera S Fredholm M Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR BMC Molecular Biology 2007, 8:67. 2000887 17697375 10.1186/1471-2199-8-67
30. Rozen S Skaletsky H Primer3 on the WWW for general users and for biologist programmers Methods Mol Biol 2000, 132:365-86. 10547847
31. Markham NR Zuker M DINAMelt web server for nucleic acid melting prediction Nucleic Acids Res 2005, 33(Web Server):W577-81. 1160267 15980540 10.1093/nar/gki591
32. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
33. Wheeler D Bhagwat M BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial Methods Mol Biol 2007, 395:149-76. 17993672
34. Chitko-McKown CG Fox JM Miller LC Heaton MP Bono JL Keen JE Grosse WM Laegreid WW Gene expression profiling of bovine macrophages in response to Escherichia coli O157:H7 lipopolysaccharide Dev Comp Immunol 2004, 28(6):635-45. 10.1016/j.dci.2003.10.002 15177116
35. Goossens K Van Poucke M Van Soom A Vandesompele J Van Zeveren A Peelman LJ Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos BMC Dev Biol 2005, 5:27. 1315359 16324220 10.1186/1471-213X-5-27
36. Spinsanti G Panti C Lazzeri E Marsili L Casini S Frati F Fossi C Selection of reference genes for quantitative RT-PCR studies) in striped dolphin: Stenella coeruleoalba) skin biopsies BMC Molecular Biology 2006, 7:32. 1599742 16984641 10.1186/1471-2199-7-32
37. Maccoux LJ Clements DN Salway F Day PJ Identification of new reference genes for the normalisation of canine osteoarthritic joint tissue transcripts from microarray data BMC Mol Biol 8, 62:2007, Jul 25. 1976117 17651481 10.1186/1471-2199-8-62
38. Solanas M Moral R Escrich E Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors Anal Biochem 2001, 288(1):99-102. 10.1006/abio.2000.4889 11141312
39. Mogal A Abdulkadir SA Effects of Histone Deacetylase Inhibitor: HDACi); Trichostatin-A: TSA) on the expression of housekeeping genes Mol Cell Probes 2006, 20(2):81-6. 10.1016/j.mcp.2005.09.008 16326072
40. Radonic A Thulke S Mackay IM Landt O Siegert W Nitsche A Guideline to reference gene selection for quantitative real-time PCR Biochem Biophys Res Commun 313, (4):856-62. 2004, Jan 23. 10.1016/j.bbrc.2003.11.177 14706621
41. Ohl F Jung M Xu C Stephan C Rabien A Burkhardt M Nitsche A Kristiansen G Loening SA Radoniæ A Jung K Gene expression studies in prostate cancer tissue: Which reference gene should be selected for normalization? J Mol Med 2005, 83(12):1014-24. 10.1007/s00109-005-0703-z 16211407
42. Szabo A Perou CM Karaca M Perreard L Quackenbush JF Bernard PS Statistical modeling for selecting housekeeper genes Genome Biol 2004, 5(8):R59. 507884 15287981 10.1186/gb-2004-5-8-r59
43. Olsvik PA Lie KK Jordal AE Nilsen TO Hordvik I Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon BMC Mol Biol 6, 21:2005 Nov 17. 1314898 16293192 10.1186/1471-2199-6-21