Selection of suitable reference genes for normalization of quantitative real-time polymerase chain reaction in human cartilage endplate of the lumbar spine

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Zhou, Zhi Jie ^a,b   Zhang, Jian Feng ^a,b   Xia, Ping ^a,b   Wang, Ji Ying ^a,b   Chen, Shuai ^a,b   Fang, Xiang Qian ^a,b   Fan, Shun Wu ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 MICROGLOBULIN; BETA ACTIN; BETA GLUCURONIDASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PORPHOBILINOGEN DEAMINASE; RNA 18S; TATA BINDING PROTEIN;

18S RRNA GENE; ACTB GENE; ALGORITHM; ARTICLE; B2M GENE; CONTROLLED STUDY; GAPDH GENE; GENE; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC STABILITY; GUSB GENE; HMBS GENE; HOUSEKEEPING GENE; HPRT1 GENE; HUMAN; HUMAN TISSUE; IPO8 GENE; LDHA GENE; LUMBAR SPINE; LUMBAR SPINE CARTILAGE ENDPLATE; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; RPL13A GENE; SDHA GENE; TBP GENE; TISSUE SPECIFICITY; CARTILAGE; GENE EXPRESSION PROFILING; LUMBAR VERTEBRA; METABOLISM; STANDARD; STANDARDS;

CARTILAGE; GENE EXPRESSION PROFILING; HUMANS; LUMBAR VERTEBRAE; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS;

EID: 84895893568     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088892     Document Type: Article

References (27)

1. Modic MT, Masaryk TJ, Ross JS, Carter JR (1988) Imaging of degenerative disk disease. Radiology 168: 177-186.
2. Jensen TS, Karppinen J, Sorensen JS, Niinimäki J, Leboeuf-Yde C (2008) Vertebral endplate signal changes (Modic change): a systematic literature review of prevalence and association with non-specific low back pain. Eur Spine J 17: 1407-1422.
3. Albert HB, Manniche C (2007) Modic changes following lumbar disc herniation. Eur Spine J 16: 977-982. (Pubitemid 47063473)
4. Zhang YH, Zhao CQ, Jiang LS, Chen XD, Dai LY (2008) Modic changes: a systematic review of the literature. Eur Spine J 17: 1289-1299.
5. Markova DZ, Kepler CK, Addya S, Murray HB, Vaccaro AR, et al. (2013) An organ culture system to model early degeneration changes of the interverbral disc II: profiling global gene expression changes. Arthritis Res Ther 15: R121.
6. Cong F, Liu X, Han Z, Shao Y, Kong X, et al. (2013) Transcriptome analysis of chicken kidney tissue following coronavirus avian infection bronchitis virus infection. BMC Genomics 2013 14: 743.
7. Mallein-Gerin F, Gouttenoire J (2004) RNA extraction from cartilage. Methods Mol Med 100: 101-104.
8. Price JS, Waters JG, Darrah C, Pennington C, Edwards DR, et al. (2002) The role of chondrocyte senescence in osteoarthritis. Aging Cell 1: 57-65.
9. Wang J, Hu L, Hamilton SR, Coombes KR, Zhang W (2003) RNA amplification strategies for cDNA microarray experiments. Biotechniques 34: 394-400. (Pubitemid 36184098)
10. Subkhankulova T, Livesey FJ (2006) Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level. Genome Biol 7: R18.
11. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalization; strategies and considerations. Genes Immun 6: 279-284. (Pubitemid 40903399)
12. Lee PD, Sladek R, Greenwood CM, Hudson TJ (2002) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12: 292-297. (Pubitemid 34162995)
13. Andersen CL, Jensen JL, Ørntoft 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. (Pubitemid 39006544)
14. Guénin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, et al. (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of reference. J Exp Bot 60: 487-493.
15. Gebhardt FM, Scott HA, Dodd PR (2010) Horsekeepers of accurate transcript expression analysis in Alzheimer's disease autopsy brain tissue. Alzheimers Dement 6: 465-474.
16. Vandesompele J, De Preter K, Patty F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: R34.
17. Pombo-Suarez M, Calaza M, Gomez-Reino JJ, Gonzalez A (2008) Reference genes for normalization of gene expression studies in human osteoarthritic articular cartilage. BMC Mol Biol 9: 17.
18. Untergasser A (2008) "RNAprep-Trizol combined with Columns" Untergasser's Lab. Available:http://www.untergasser.de/lab/protocols/rna-prep- comb-trizol-v1-0.htm. Accessed 18 January 2012.
19. Bustin SA (2010) Why the need for qPCR publication guidelines?-The case for MIQE. Methods 50: 217-226.
20. Karlsson C, Dehne T, Lindahl A, Brittberg M, Pruss A, et al. (2010) Genome-wide expression profiling reveals new candidate genes associated with osteoarthritis. Osteoarthritis Cartilage 18: 581-592.
21. Dehne T, Karlsson C, Ringe J, Sittinger M, Lindahl A (2009) Chondrogenic differentiation potential of osteoarthritic chondrocytes and their possible use in matrix-associated autologous chondrocyte transplantation. Arthritis Res Ther 11: R133.
22. 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. (Pubitemid 38448421)
23. Chen D, Pan X, Xiao P, Farwell MA, Zhang B (2011) Evaluation and identification of reliable reference genes for pharmacogenomics, toxicogenomics and small RNA expression analysis. J Cell Physiol 226: 2469-2477.
24. Warzybok A, Migocka M (2013) Reliable reference genes for normalization of gene expression in cucumber grown under different nitrogen nutrition. Plos One 8: e2887.
25. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, et al. (2004) Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37: 112-114.
26. Ren S, Zhang F, Li C, Jia C, Li S, et al. (2010) Selection of housekeeping genes for use in quantitative reverse transcription PCR assays on the murine cornea. Mol Vis 16: 1076-1086.
27. Ko CS, Huang JP, Huang CW, Chu IM (2009) Type II collagen-chondroitin sulfate-hyaluronan scaffold cross-linked by genipin for cartilage tissue engineering. J Biosic Bioeng 107: 177-182.