Terminal continuation (TC) RNA amplification without second strand synthesis

Journal of Neuroscience Methods

Volumn 177, Issue 2, 2009, Pages 381-385

  Alldred, Melissa J ^a   Che, Shaoli ^a,b   Ginsberg, Stephen D ^a,b  

^a NATHAN S KLINE INSTITUTE FOR PSYCHIATRIC RESEARCH   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alzheimer's disease; In vitro transcription; Microarray; qPCR; RNA amplification

Indexed keywords

DNA; RNA;

AGED; ALZHEIMER DISEASE; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN NERVE CELL; CADAVER; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DNA SYNTHESIS; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIPPOCAMPUS; HUMAN; HUMAN TISSUE; LASER CAPTURE MICRODISSECTION; MALE; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA STRUCTURE; TERMINAL CONTINUATION RNA AMPLIFICATION;

AGED; AGED, 80 AND OVER; ALZHEIMER DISEASE; ANIMALS; BRAIN; BRAIN CHEMISTRY; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; MALE; MICE; MICE, INBRED C57BL; MICRODISSECTION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA;

EID: 58149488782     PISSN: 01650270     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2008.10.027     Document Type: Article

References (30)

1. ABI, 2004. Guide to performing relative quantitation of gene expression using real-time quantitative PCR. Applied biosystems product guide, ABI Press, Foster City, pp. 1-60.
2. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25 (2000) 169-193
3. Callahan L.M., Vaules W.A., and Coleman P.D. Quantitative decrease in synaptophysin message expression and increase in cathepsin D message expression in Alzheimer disease neurons containing neurofibrillary tangles. J. Neuropathol. Exp. Neurol. 58 (1999) 275-287
4. Che S., and Ginsberg S.D. Amplification of transcripts using terminal continuation. Lab. Invest. 84 (2004) 131-137
5. Dafforn A., Chen P., Deng G., Herrler M., Iglehart D., Koritala S., et al. Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. BioTechniques 37 (2004) 854-857
6. Eberwine J., Kacharmina J.E., Andrews C., Miyashiro K., McIntosh T., Becker K., et al. mRNA expression analysis of tissue sections and single cells. J. Neurosci. 21 (2001) 8310-8314
7. Eberwine J., Yeh H., Miyashiro K., Cao Y., Nair S., Finnell R., et al. Analysis of gene expression in single live neurons. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 3010-3014
8. Ginsberg S.D. RNA amplification strategies for small sample populations. Methods 37 (2005) 229-237
9. Ginsberg S.D. Transcriptional profiling of small samples in the central nervous system. Methods Mol. Biol. 439 (2008) 147-158
10. Ginsberg S.D., and Che S. Expression profile analysis within the human hippocampus: comparison of CA1 and CA3 pyramidal neurons. J. Comp. Neurol. 487 (2005) 107-118
11. Ginsberg S.D., and Che S. RNA amplification in brain tissues. Neurochem. Res. 27 (2002) 981-992
12. Ginsberg S.D., Che S., Counts S.E., and Mufson E.J. Shift in the ratio of three-repeat tau and four-repeat tau mRNAs in individual cholinergic basal forebrain neurons in mild cognitive impairment and Alzheimer's disease. J. Neurochem. 96 (2006) 1401-1408
13. Ginsberg S.D., Che S., Wuu J., Counts S.E., and Mufson E.J. Down regulation of trk but not p75 gene expression in single cholinergic basal forebrain neurons mark the progression of Alzheimer's disease. J. Neurochem. 97 (2006) 475-487
14. Ginsberg S.D., Crino P.B., Lee V.M.-Y., Eberwine J.H., and Trojanowski J.Q. Sequestration of RNA in Alzheimer's disease neurofibrillary tangles and senile plaques. Ann. Neurol. 41 (1997) 200-209
15. Ginsberg S.D., Hemby S.E., Lee V.M.-Y., Eberwine J.H., and Trojanowski J.Q. Expression profile of transcripts in Alzheimer's disease tangle-bearing CA1 neurons. Ann. Neurol. 48 (2000) 77-87
16. Ginsberg S.D., and Mirnics K. Functional genomic methodologies. Prog. Brain Res. 158 (2006) 15-40
17. Goff L.A., Bowers J., Schwalm J., Howerton K., Getts R.C., and Hart R.P. Evaluation of sense-strand mRNA amplification by comparative quantitative PCR. BMC Genom. 5 (2004) 76
18. Gutala R.V., and Reddy P.H. The use of real-time PCR analysis in a gene expression study of Alzheimer's disease post-mortem brains. J. Neurosci. Methods 132 (2004) 101-107
19. Hyman B.T., and Trojanowski J.Q. Consensus recommendations for the postmortem diagnosis of Alzheimer disease from the National Institute on Aging and the Reagan Institute Working Group on diagnostic criteria for the neuropathological assessment of Alzheimer disease. J. Neuropathol. Exp. Neurol. 56 (1997) 1095-1097
20. Iscove N.N., Barbara M., Gu M., Gibson M., Modi C., and Winegarden N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 20 (2002) 940-943
21. Kacharmina J.E., Crino P.B., and Eberwine J. Preparation of cDNA from single cells and subcellular regions. Methods Enzymol. 303 (1999) 3-18
22. Knobloch M., and Mansuy I.M. Dendritic spine loss and synaptic alterations in Alzheimer's disease. Mol. Neurobiol. 37 (2008) 73-82
23. Kurn N., Chen P., Heath J.D., Kopf-Sill A., Stephens K.M., and Wang S. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin. Chem. 51 (2005) 1973-1981
24. Matz M., Shagin D., Bogdanova E., Britanova O., Lukyanov S., Diatchenko L., et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27 (1999) 1558-1560
25. Mirra S.S., Heyman A., McKeel D., Sumi S.M., Crain B.J., Brownlee L.M., et al. The Consortium to Establish a Registry for Alzheimer's Disease (CERAD). Part II. Standardization of the neuropathologic assessment of Alzheimer's disease. Neurology 41 (1991) 479-486
26. Nygaard V., and Hovig E. Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res. 34 (2006) 996-1014
27. Schneider J., Buness A., Huber W., Volz J., Kioschis P., Hafner M., et al. Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments. BMC Genom. 5 (2004) 29
28. VanGelder R., von Zastrow M., Yool A., Dement W., Barchas J., and Eberwine J. Amplified RNA (aRNA) synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. U.S.A. 87 (1990) 1663-1667
29. Wang E., Miller L.D., Ohnmacht G.A., Liu E.T., and Marincola F.M. High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18 (2000) 457-459
30. Zhumabayeva B., Diatchenko L., Chenchik A., and Siebert P.D. Use of SMART-generated cDNA for gene expression studies in multiple human tumors. BioTechniques 30 (2001) 158-163