New selected
normalisation papers:
Evaluation of
Normalization Strategies Used in Real-Time
Quantitative PCR Experiments in HepaRG Cell Line
Studies.
Ceelen L, De Craene J, De Spiegelaere W.
Pathlicon nv, Evergem, Belgium
Clin Chem. 2013 Sep 11. (Epub ahead of print)
Reference genes in
real-time PCR
Bartlomiej Kozera & Marcin Rapacz
J Appl Genet. 2013 Sep 28. (Epub ahead of print)
A critique of widely
used normalization software tools and an
alternative method to identify reliable reference
genes in red clover (Trifolium pratense L.)
Khosro Mehdi Khanlou and Erik Van Bockstaele
Planta. 2012 Nov;236(5): 1381-1393
GENE EXPRESSION
STUDIES: HOW TO OBTAIN ACCURATE AND RELIABLE DATA
BY QUANTITATIVE REAL-TIME RT PCR
Jelena Nestorov1, Gordana Mati1, Ivana Elakovi1,
Nikola Tani2
1 Department of Biochemistry
2 Department of Neurobiology, Institute for Biological
Research, University of Belgrade, Belgrade, Serbia
J Med Biochem 32: 325–338, 2013 (Review article)
Application of qRT-PCR
and RNA-Seq analysis for the identification of
housekeeping genes useful for normalization of
gene expression values during hermonthica
development
M. Fernadez-Aparicio, K. Huang, E. K. Wafula, A.
Honaas, N. J. Wickett, M. P. Timko, C. W. dePamphilis,
J. I. Yoder, J H. Westwood
Mol Biol Rep (2013) 40:3395–3407
Read_qPCR and
Norm_qPCR: R packages for the reading, quality
checking and normalisation of RT-qPCR
quantification cycle (Cq) data.
Perkins JR, Dawes JM, McMahon SB, Bennett DL, Orengo
C, Kohl M.
BMC Genomics. 2012 Jul 2;13: 296
Selection of novel
reference genes for use in the human central
nervous system: a BrainNet Europe Study.
Durrenberger PF, Fernando FS, Magliozzi R, Kashefi SN,
Bonnert TP, Ferrer I, Seilhean D, Nait-Oumesmar B,
Schmitt A, Gebicke-Haerter PJ, Falkai P, Grünblatt E,
Palkovits M, Parchi P, Capellari S, Arzberger T,
Kretzschmar H, Roncaroli F, Dexter DT, Reynolds R.
Wolfson Neuroscience Laboratories, Division of Brain
Sciences, Imperial College London, Hammersmith
Hospital Campus, London, UK.
Acta Neuropathol. 2012 Dec;124(6): 893-903
Mixed modeling and
sample size calculations for identifying
housekeeping genes
Hongying Dai, Richard Charnigo, Carrie A. Vyhlidal,
Bridgette L. Jonesc and Madhusudan Bhandary
Statist. Med. 2013
Gene-family profiling:
a normalization-free real-time RT-PCR approach
with increased physiological resolution
Stian Ellefsen and Kare-Olav Stenslokken
1 Lillehammer University College, Lillehamme
2 Institute of Clinical Medicine, and 3Department of
Molecular Biosciences, University of Oslo, Oslo,
Norway
Physiol Genomics 42: 1–4, 2010
A Novel Strategy for
Selection and Validation of Reference Genes in
Dynamic Multidimensional Experimental Design in
Yeast
Ayca Cankorur-Cetinkaya, Elif Dereli, Serpil Eraslan,
Erkan Karabekmez, Duygu Dikicioglu, Betul Kirdar
Department of Chemical Engineering, Bogazici
University, Bebek, Istanbul, Turkey
PLoS ONE, 2012, Volume 7, Issue 6, e38351
A simple analytical and
experimental procedure for selection of reference
genes for reverse-transcription quantitative PCR
normalization data
R. Manjarin, N. L. Trottier, P. S. Weber, J. S.
Liesman, N. P. Taylor, and J. P. Steibel
Department of Animal Science,
Department of Large Animal Clinical Sciences, and
Department of Fisheries and Wildlife, Michigan State
University, East Lansing 48824
J. Dairy Sci. 94 :4950–4961
NORMA-Gene: A simple
and robust method for qPCR normalization based on
target gene data
Lars-Henrik Heckmann, Peter B Sørensen, Paul Henning
Krogh and Jesper G Sørensen
National Environmental Research Institute, Aarhus
University, Department of Terrestrial Ecology,
Vejlsøvej 25, DK-8600 Silkeborg, Denmark
BMC Bioinformatics 2011, 12: 250
Accurate RT-qPCR gene
expression analysis on cell culture lysates
Gert Van Peer, Pieter Mestdagh & Jo Vandesompele
SCIENTIFIC REPORTS (2012) 2: 222
RefGenes:
identification of reliable and condition specific
reference genes for RT-qPCR data normalization.
Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S,
Borghi L, Verbrugghe P, Kalaydjieva L, Bleuler S,
Laule O, Descombes P, Gruissem W, Zimmermann P.
BMC Genomics. 2011 Mar 21;12(1):156.
Identification of
suitable reference genes for normalization of qPCR
data in comparative transcriptomics analyses in
the Triticeae
Marıa J. Gimenez, Fernando Piston, Sergio G. Atienza
Planta. 2011 233(1):163-73.
Evaluation of suitable
reference genes for normalization of real-time
reverse transcription PCR analysis in colon cancer
Lise Aa Sorby, Solveig N Andersen, Ida RK Bukholm,
Morten B Jacobsen
Journal of Experimental & Clinical Cancer Research
2010, 29:144
Tissue-specific
disallowance of housekeeping genes: The other face
of cell differentiation
Lieven Thorrez, Ilaria Laudadio, Katrijn Van Deun,
Roel Quintens, Nico Hendrickx, Mikaela Granvik,
Katleen Lemaire, Anica Schraenen, Leentje Van Lommel,
Stefan Lehnert, Cristina Aguayo-Mazzucato, Rui
Cheng-Xue, Patrick Gilon, Iven Van Mechelen, Susan
Bonner-Weir, Fre´de´ric Lemaigre, and Frans Schuit
Genome Research 2011 21:95–105
Robust RT-qPCR Data
Normalization: Validation and Selection of
Internal Reference Genes during Post-Experimental
Data Analysis
Daijun Ling, Paul M. Salvaterra
PLoS ONE 2011 6(3): e17762.
Identification of genes
for normalization of quantitative real-time PCR
data in ovarian tissues
Jie Fu, Lihong Bian, Li Zhao, Zhouhuan Dong, Xin Gao,
Haofei Luan, Yunjuan Sun, and Haifeng Song
Acta Biochim Biophys Sin (2010): 1–7
A pipeline to determine
RT-QPCR control genes for evolutionary studies:
application to primate gene expression across
multiple tissues.
Fedrigo O, Warner LR, Pfefferle AD, Babbitt CC,
Cruz-Gordillo P, Wray GA.
PLoS One. 2010 5(9). pii: e12545.
Selection of reference
genes for quantitative polymerase chain reaction
studies in purified B cells from B cell chronic
lymphocytic leukaemia patients.
Valceckiene V, Kontenyte R, Jakubauskas A,
Griskevicius L.
Br J Haematol. 2010 Nov;151(3):232-8.
Validation of rat
reference genes for improved quantitative gene
expression analysis using low density arrays
Jenny Hong Cai, Shibing Deng, Steven W. Kumpf,
Patricia A. Lee, Panayiotis Zagouras, Anne Ryan, and
Dan S. Gallagher
BioTechniques 2010 42:503-512
Identification of
suitable internal control genes for expression
studies in Coffea arabica under different
experimental conditions.
Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia
IG.
BMC Mol Biol. 2009 Jan 6;10:1
Selection of reliable
reference genes for gene expression studies in
peach using real-time PCR
Zhaoguo Tong, Zhihong Gao, Fei Wang, Jun Zhou and Zhen
Zhang
BMC Molecular Biology 2009, 10:71
Evaluation of reference
genes for studies of gene expression in the bovine
liver, kidney, pituitary, and thyroid
Pawe Lisowski, Mariusz Pierzcha, Joanna Gooecik,
Chandra S. Pareek, Lech Zwierzchowski
J Appl Genet 49(4), 2008, pp. 367–37
Data-driven
normalization strategies for high-throughput
quantitative RT-PCR
Jessica C Mar, Yasumasa Kimura, Kate Schroder,
Katharine M Irvine, Yoshihide Hayashizaki, Harukazu
Suzuki, David Hume and John Quackenbush
BMC Bioinformatics 2009, 10:110
An abundance of
ubiquitously expressed genes revealed by tissue
transcriptome sequence data.
Ramsköld D, Wang ET, Burge CB, Sandberg R.
PLoS Comput Biol. 2009 5(12):e1000598
'Desperate house
genes': the dramatic example of hypoxia.
Caradec J, Sirab N, Keumeugni C, Moutereau S,
Chimingqi M, Matar C, Revaud D, Bah M, Manivet P,
Conti M, Loric S.
Br J Cancer. 2010 Mar 16;102(6):1037-43. Epub 2010 Feb
23.
Reference gene
alternatives to Gapdh in rodent and human heart
failure gene expression studies.
Brattelid T, Winer LH, Levy FO, Liestøl K, Sejersted
OM, Andersson KB.
BMC Mol Biol. 2010 Mar 23;11:22.
Genomic selection of
reference genes for real-time PCR in human
myocardium.
Pilbrow AP, Ellmers LJ, Black MA, Moravec CS, Sweet
WE, Troughton RW, Richards AM, Frampton CM, Cameron
VA.
BMC Med Genomics. 2008 Dec 29;1:64.
Selection of
internal control genes for quantitative real-time
RT-PCR studies during tomato development process.
Expósito-Rodríguez M, Borges AA, Borges-Pérez A, Pérez
JA.
BMC Plant Biol. 2008 Dec 22;8:131.
Validation of putative
reference genes for gene expression studies in
human hepatocellular carcinoma using real-time
quantitative RT-PCR.
Cicinnati VR, Shen Q, Sotiropoulos GC, Radtke A,
Gerken G, Beckebaum S.
BMC Cancer. 2008 8:350.
Characterization of
housekeeping genes in zebrafish: male-female
differences and effects of tissue type,
developmental stage and chemical treatment.
McCurley AT, Callard GV.
BMC Mol Biol. 2008 9:102.
Optimisation of
region-specific reference gene selection and
relative gene expression analysis methods for
pre-clinical trials of Huntington's disease.
Benn CL, Fox H, Bates GP.
Mol Neurodegener. 2008 3:17.
The lack of a
systematic validation of reference genes: a
serious pitfall undervalued in reverse
transcription-polymerase chain reaction (RT-PCR)
analysis in plants.
Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre
JF, Louvet R, Rusterucci C, Moritz T, Guerineau F,
Bellini C, Van Wuytswinkel O.
Plant Biotechnol J. 2008 6(6):609-18
Normalization of
qRT-PCR data: the necessity of adopting a
systematic, experimental conditions-specific,
validation of references.
Guénin S, Mauriat M, Pelloux J, Van Wuytswinkel O,
Bellini C, Gutierrez L.
J Exp Bot. 2009 60(2):487-93. Review
Selection of
optimal reference genes for normalization in
quantitative RT-PCR.
Chervoneva I, Li Y, Schulz S, Croker S, Wilson C,
Waldman SA, Hyslop T.
BMC Bioinformatics. 2010 11:253.
Validation
of the comparative quantification method of
real-time PCR analysis and a cautionary tale of
housekeeping gene selection
Richard D. McCurdy, John J. McGrath, Alan Mackay-Sim
Gene Ther Mol Biol Vol 12, 15-24, 2008
Gene expression results
in lipopolysaccharide-stimulated monocytes depend
significantly on the choice of reference genes.
Piehler AP, Grimholt RM, Ovstebø R, Berg JP.
BMC Immunol. 2010 11:21.
Selection of
housekeeping genes for use in quantitative reverse
transcription PCR assays on the murine cornea.
Shengwei Ren, Feng Zhang, Changyou Li, Changkai Jia,
Siyuan Li, Haijie Xi, Hongbo Zhang, Lingling Yang,
Yiqiang Wang
Molecular Vision 2010; 16:1076-1086
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