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Volumn 203, Issue 1-3, 2010, Pages 76-82

Postmortem mRNA profiling II: Practical considerations

Author keywords

Data interpretation; MRNA profiling; Postmortem tissue; Sample handling and processing

Indexed keywords

DNA; MESSENGER RNA; RIBONUCLEASE;

EID: 78649317875     PISSN: 03790738     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.forsciint.2010.07.007     Document Type: Article
Times cited : (25)

References (45)
  • 1
    • 41049086156 scopus 로고    scopus 로고
    • Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues
    • Popova T., Mennerich D., Weith A., Quast K. Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues. BMC Genomics 2008, 25(9):91.
    • (2008) BMC Genomics , vol.25 , Issue.9 , pp. 91
    • Popova, T.1    Mennerich, D.2    Weith, A.3    Quast, K.4
  • 3
    • 0015209392 scopus 로고
    • Properties of mouse globin messenger ribonucleic acid and its preparation in milligram quantities
    • Williamson R., Morrison M., Lanyon G., Eason R., Paul J. Properties of mouse globin messenger ribonucleic acid and its preparation in milligram quantities. Biochemistry 1971, 10:3014-3021.
    • (1971) Biochemistry , vol.10 , pp. 3014-3021
    • Williamson, R.1    Morrison, M.2    Lanyon, G.3    Eason, R.4    Paul, J.5
  • 4
    • 10744228401 scopus 로고    scopus 로고
    • Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain
    • Tomita H., Vawter M.P., Walsh D.M., et al. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol. Psychiatry 2004, 55:346-352.
    • (2004) Biol. Psychiatry , vol.55 , pp. 346-352
    • Tomita, H.1    Vawter, M.P.2    Walsh, D.M.3
  • 5
    • 34249889834 scopus 로고    scopus 로고
    • Methodological considerations for gene expression profiling of human brain
    • Atz M., Walsh D., Cartagena P., et al. Methodological considerations for gene expression profiling of human brain. J. Neurosci. Methods 2007, 163:295-309.
    • (2007) J. Neurosci. Methods , vol.163 , pp. 295-309
    • Atz, M.1    Walsh, D.2    Cartagena, P.3
  • 7
    • 0035189199 scopus 로고    scopus 로고
    • Neuropeptide Y (NPY) mRNA in rat brain tissue: effects of decapitation and high-energy microwave irradiation on post mortem stability
    • Thorsell A., Gruber S.H., Mathé A.A., Heilig M. Neuropeptide Y (NPY) mRNA in rat brain tissue: effects of decapitation and high-energy microwave irradiation on post mortem stability. Neuropeptides 2001, 35:168-173.
    • (2001) Neuropeptides , vol.35 , pp. 168-173
    • Thorsell, A.1    Gruber, S.H.2    Mathé, A.A.3    Heilig, M.4
  • 9
    • 0033775615 scopus 로고    scopus 로고
    • Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    • Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 2000, 25:169-193.
    • (2000) J. Mol. Endocrinol. , vol.25 , pp. 169-193
    • Bustin, S.A.1
  • 10
  • 11
    • 14044265394 scopus 로고    scopus 로고
    • Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction
    • Bustin S.A., Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech. 2004, 15:155-166.
    • (2004) J. Biomol. Tech. , vol.15 , pp. 155-166
    • Bustin, S.A.1    Nolan, T.2
  • 12
    • 34547650893 scopus 로고    scopus 로고
    • Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology
    • Weis S., Llenos I.C., Dulay J.R., Elashoff M., Martínez-Murillo F., Miller C.L. Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology. J. Neurosci. Methods 2007, 165:198-209.
    • (2007) J. Neurosci. Methods , vol.165 , pp. 198-209
    • Weis, S.1    Llenos, I.C.2    Dulay, J.R.3    Elashoff, M.4    Martínez-Murillo, F.5    Miller, C.L.6
  • 13
    • 33748095919 scopus 로고    scopus 로고
    • Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR
    • Fleige S., Walf V., Huch S., Prgomet C., Sehm J., Pfaffl M.W. Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol. Lett. 2006, 28:1601-1613.
    • (2006) Biotechnol. Lett. , vol.28 , pp. 1601-1613
    • Fleige, S.1    Walf, V.2    Huch, S.3    Prgomet, C.4    Sehm, J.5    Pfaffl, M.W.6
  • 15
    • 0033986177 scopus 로고    scopus 로고
    • A microfluidic system for high-speed reproducible DNA sizing and quantitation
    • Mueller O., Hahnenberger K., Dittmann M., et al. A microfluidic system for high-speed reproducible DNA sizing and quantitation. Electrophoresis 2000, 21:128-134.
    • (2000) Electrophoresis , vol.21 , pp. 128-134
    • Mueller, O.1    Hahnenberger, K.2    Dittmann, M.3
  • 16
    • 0036668567 scopus 로고    scopus 로고
    • Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems
    • Bustin S.A. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 2002, 29:23-39.
    • (2002) J. Mol. Endocrinol. , vol.29 , pp. 23-39
    • Bustin, S.A.1
  • 17
    • 33645241407 scopus 로고    scopus 로고
    • The RIN: an RNA integrity number for assigning integrity values to RNA measurements
    • Schroeder A., Mueller O., Stocker S., et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 2006, 7:3-16.
    • (2006) BMC Mol. Biol. , vol.7 , pp. 3-16
    • Schroeder, A.1    Mueller, O.2    Stocker, S.3
  • 18
    • 85168040399 scopus 로고    scopus 로고
    • Post mortem mRNA profiling I: possibilities and limitations, this issue
    • M. Vennemann, A. Koppelkamm, Post mortem mRNA profiling I: possibilities and limitations, this issue.
    • Vennemann, M.1    Koppelkamm, A.2
  • 19
    • 45449087921 scopus 로고    scopus 로고
    • QBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
    • Hellemans J., Mortier G., De Paepe A., Speleman F., Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007, 8:R19.
    • (2007) Genome Biol. , vol.8
    • Hellemans, J.1    Mortier, G.2    De Paepe, A.3    Speleman, F.4    Vandesompele, J.5
  • 20
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method
    • Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 2001, 25:402-408.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 21
    • 21344471138 scopus 로고    scopus 로고
    • Real-time RT-PCR normalisation: strategies and considerations
    • Huggett J., Dheda K., Bustin S., Zumla A. Real-time RT-PCR normalisation: strategies and considerations. Genes Immun. 2005, 6:279-284.
    • (2005) Genes Immun. , vol.6 , pp. 279-284
    • Huggett, J.1    Dheda, K.2    Bustin, S.3    Zumla, A.4
  • 22
    • 27644563899 scopus 로고    scopus 로고
    • The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization
    • Dheda K., Huggett J.F., Chang J.S., Kim L.U., Bustin S.A., Johnson M.A., Rook G.A., Zumla A. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal. Biochem. 2005, 344:141-143.
    • (2005) Anal. Biochem. , vol.344 , pp. 141-143
    • Dheda, K.1    Huggett, J.F.2    Chang, J.S.3    Kim, L.U.4    Bustin, S.A.5    Johnson, M.A.6    Rook, G.A.7    Zumla, A.8
  • 24
    • 4344564046 scopus 로고    scopus 로고
    • Comparison of reverse transcriptases in gene expression analysis
    • Ståhlberg A., Kubista M., Pfaffl M. Comparison of reverse transcriptases in gene expression analysis. Clin. Chem. 2004, 50:1678-1680.
    • (2004) Clin. Chem. , vol.50 , pp. 1678-1680
    • Ståhlberg, A.1    Kubista, M.2    Pfaffl, M.3
  • 25
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • RESEARCH0034
    • 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 Biol. 2002, 3. RESEARCH0034.
    • (2002) Genome Biol. , vol.3
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3    Poppe, B.4    Van Roy, N.5    De Paepe, A.6    Speleman, F.7
  • 26
    • 33747889223 scopus 로고    scopus 로고
    • Use of external controls in microarray experiments
    • Yang I.V. Use of external controls in microarray experiments. Methods Enzymol. 2006, 411:50-63.
    • (2006) Methods Enzymol. , vol.411 , pp. 50-63
    • Yang, I.V.1
  • 28
    • 3042561451 scopus 로고    scopus 로고
    • Evaluation of five different cDNA labeling methods for microarrays using spike controls
    • Badiee A., Eiken H.G., Steen V.M., Løvlie R. Evaluation of five different cDNA labeling methods for microarrays using spike controls. BMC Biotechnol. 2003, 3:23.
    • (2003) BMC Biotechnol. , vol.3 , pp. 23
    • Badiee, A.1    Eiken, H.G.2    Steen, V.M.3    Løvlie, R.4
  • 32
    • 34248594099 scopus 로고    scopus 로고
    • Real-time PCR detection of five different " endogenous control gene" transcripts in forensic autopsy material
    • June
    • Heinrich M., Lutz-Bonengel S., Matt K., Schmidt U. Real-time PCR detection of five different " endogenous control gene" transcripts in forensic autopsy material. Forensic Sci. Int. Genet. 2007, 1(June (2)):163-169.
    • (2007) Forensic Sci. Int. Genet. , vol.1 , Issue.2 , pp. 163-169
    • Heinrich, M.1    Lutz-Bonengel, S.2    Matt, K.3    Schmidt, U.4
  • 33
    • 85027933045 scopus 로고    scopus 로고
    • Validation of adequate endogenous reference genes for the normalisation of qPCR gene expression data in human post mortem tissue
    • March 19 [Epub ahead of print]
    • Koppelkamm A., Vennemann B., Fracasso T., Lutz-Bonengel S., Schmidt U., Heinrich M Validation of adequate endogenous reference genes for the normalisation of qPCR gene expression data in human post mortem tissue. Int. J. Legal Med. 2010, March 19 [Epub ahead of print].
    • (2010) Int. J. Legal Med.
    • Koppelkamm, A.1    Vennemann, B.2    Fracasso, T.3    Lutz-Bonengel, S.4    Schmidt, U.5    Heinrich, M.6
  • 34
    • 67649444944 scopus 로고    scopus 로고
    • Reference gene validation software for improved normalization
    • Caister Academic Press, J. Logan, K. Edwards, N. Saunders (Eds.)
    • Vandesompele J., Kubista M., Pfaffl M.W. Reference gene validation software for improved normalization. Real-Time PCR: Current Technology and Applications 2009, 48-64. Caister Academic Press. J. Logan, K. Edwards, N. Saunders (Eds.).
    • (2009) Real-Time PCR: Current Technology and Applications , pp. 48-64
    • Vandesompele, J.1    Kubista, M.2    Pfaffl, M.W.3
  • 35
    • 3442876969 scopus 로고    scopus 로고
    • 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
    • Andersen C.L., Jensen J.L., Ørntoft T.F. 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.
    • (2004) Cancer Res. , vol.64 , pp. 5245-5250
    • Andersen, C.L.1    Jensen, J.L.2    Ørntoft, T.F.3
  • 36
    • 1842483281 scopus 로고    scopus 로고
    • Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-excel-based tool using pair-wise correlations
    • Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-excel-based tool using pair-wise correlations. Biotechnol. Lett. 2004, 26:509-515.
    • (2004) Biotechnol. Lett. , vol.26 , pp. 509-515
    • Pfaffl, M.W.1    Tichopad, A.2    Prgomet, C.3    Neuvians, T.P.4
  • 37
    • 28344434302 scopus 로고    scopus 로고
    • Data analysis and interpretation
    • International University Line, La Jolla, CA, S.A. Bustin (Ed.)
    • Bustin S.A., Nolan T. Data analysis and interpretation. A-Z of Quantitative PCR. IUL Biotechnology Series 5 2004, International University Line, La Jolla, CA. S.A. Bustin (Ed.).
    • (2004) A-Z of Quantitative PCR. IUL Biotechnology Series 5
    • Bustin, S.A.1    Nolan, T.2
  • 38
    • 77649233414 scopus 로고    scopus 로고
    • Why the need for qPCR publication guidelines?-the case for MIQE
    • Bustin S.A. Why the need for qPCR publication guidelines?-the case for MIQE. Methods 2010, 50:217-226.
    • (2010) Methods , vol.50 , pp. 217-226
    • Bustin, S.A.1
  • 40
    • 74049156876 scopus 로고    scopus 로고
    • Effects of antemortem and postmortem variables on human brain mRNA quality: a BrainNet Europe study
    • Durrenberger P.F., Fernando S., Kashefi S.N., et al. Effects of antemortem and postmortem variables on human brain mRNA quality: a BrainNet Europe study. J. Neuropathol. Exp. Neurol. 2010, 69:70-81.
    • (2010) J. Neuropathol. Exp. Neurol. , vol.69 , pp. 70-81
    • Durrenberger, P.F.1    Fernando, S.2    Kashefi, S.N.3
  • 41
    • 17344392308 scopus 로고    scopus 로고
    • A new mathematical model for relative quantification in real-time RT-PCR
    • Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:e45.
    • (2001) Nucleic Acids Res. , vol.29
    • Pfaffl, M.W.1
  • 42
    • 0036581160 scopus 로고    scopus 로고
    • Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR
    • Pfaffl M.W., Horgan G.W., Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. NAR 2002, 30:e36.
    • (2002) NAR , vol.30
    • Pfaffl, M.W.1    Horgan, G.W.2    Dempfle, L.3
  • 43
    • 0141957335 scopus 로고    scopus 로고
    • Quantifying mRNA in postmortem human brain: influence of gender, age at death, postmortem interval, brain pH, agonal state and inter-lobe mRNA variance
    • Preece P., Cairns N.J. Quantifying mRNA in postmortem human brain: influence of gender, age at death, postmortem interval, brain pH, agonal state and inter-lobe mRNA variance. Brain Res. Mol. Brain Res. 2003, 118:60-71.
    • (2003) Brain Res. Mol. Brain Res. , vol.118 , pp. 60-71
    • Preece, P.1    Cairns, N.J.2
  • 44
    • 4444337502 scopus 로고    scopus 로고
    • Mathematics of quantitative kinetic PCR and the application of standard curves
    • Rutledge R.G., Côté C. Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res. 2003, 31:e93.
    • (2003) Nucleic Acids Res. , vol.31
    • Rutledge, R.G.1    Côté, C.2


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