3,882
Views
31
CrossRef citations to date
0
Altmetric
Original Research

Properties of targeted preamplification in DNA and cDNA quantification

, , , , , & show all

References

  • Dalerba P, Kalisky T, Sahoo D, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 2011;29(12):1120-7
  • Guo G, Huss M, Tong GQ, et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell 2010;18(4):675-85
  • Norrman K, Strombeck A, Semb H, Stahlberg A. Distinct gene expression signatures in human embryonic stem cells differentiated towards definitive endoderm at single-cell level. Methods 2012;59(1):59-70
  • Patel AP, Tirosh I, Trombetta JJ, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 2014;344(6190):1396-401
  • Bengtsson M, Stahlberg A, Rorsman P, Kubista M. Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 2005;15(10):1388-92
  • Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008;135(2):216-26
  • Brady G, Barbara M, Iscove NN. Representative in Vitro cDNA Amplification From Individual Hemopoietic Cells and Colonies. Methods Mol Cell Biol 1990;2:17-25
  • Eberwine J, Yeh H, Miyashiro K, et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 1992;89(7):3010-14
  • Lao K, Xu NL, Sun YA, et al. Real time PCR profiling of 330 human micro-RNAs. Biotechnol J 2007;2(1):33-5
  • Lao K, Xu NL, Yeung V, et al. Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Commun 2006;343(1):85-9
  • Livak KJ, Wills QF, Tipping AJ, et al. Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods 2012;59(1):71-9
  • Rusnakova V, Honsa P, Dzamba D, et al. Heterogeneity of astrocytes: from development to injury - single cell gene expression. PLoS One 2013;8(8):e69734
  • Tang F, Hajkova P, Barton SC, et al. MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res 2006;34(2):e9
  • Stahlberg A, Kubista M. The workflow of single-cell expression profiling using quantitative real-time PCR. Expert Rev Mol Diagn 2014;14(3):323-31
  • Kojima Y, Acar A, Eaton EN, et al. Autocrine TGF-beta and stromal cell-derived factor-1 (SDF-1) signaling drives the evolution of tumor-promoting mammary stromal myofibroblasts. Proc Natl Acad Sci USA 2010;107(46):20009-14
  • Stahlberg A, Bengtsson M, Hemberg M, Semb H. Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells. Clin Chem 2009;55(12):2162-70
  • Stahlberg A, Thomsen C, Ruff D, Aman P. Quantitative PCR analysis of DNA, RNAs, and proteins in the same single cell. Clin Chem 2012;58(12):1682-91
  • Ye J, Coulouris G, Zaretskaya I, et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 2012;13:134
  • Kubista M, Andrade JM, Bengtsson M, et al. The real-time polymerase chain reaction. Mol Aspects Med 2006;27(2-3):95-125
  • Stahlberg A, Andersson D, Aurelius J, et al. Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations. Nucleic Acids Res 2011;39(4):e24
  • Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009;55(4):611-22
  • Stahlberg A, Rusnakova V, Forootan A, et al. RT-qPCR work-flow for single-cell data analysis. Methods 2013;59(1):80-8
  • SciencePrimer.com. Available from: http://scienceprimer.com/copy-number-calculator-for-realtime-pcr
  • Stahlberg A, Kubista M, Aman P. Single-cell gene-expression profiling and its potential diagnostic applications. Expert Rev Mol Diagn 2011;11(7):735-40
  • Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med 2014;6(224):224ra224
  • Pantel K, Alix-Panabieres C. Real-time liquid biopsy in cancer patients: fact or fiction? Cancer Res 2013;73(21):6384-8
  • Alix-Panabieres C, Pantel K. Challenges in circulating tumour cell research. Nat Rev Cancer 2014;14(9):623-31
  • Motz M, Paabo S, Kilger C. Improved cycle sequencing of GC-rich templates by a combination of nucleotide analogs. Biotechniques 2000;29(2):268-70
  • Musso M, Bocciardi R, Parodi S, et al. Betaine, dimethyl sulfoxide, and 7-deaza-dGTP, a powerful mixture for amplification of GC-rich DNA sequences. J Mol Diagnost 2006;8(5):544-50
  • Olive DM, Simsek M, Al-Mufti S. Polymerase chain reaction assay for detection of human cytomegalovirus. J Clin Microbiol 1989;27(6):1238-42
  • Henke W, Herdel K, Jung K, et al. Betaine improves the PCR amplification of GC-rich DNA sequences. Nucleic Acids Res 1997;25(19):3957-8
  • Kang J, Lee MS, Gorenstein DG. The enhancement of PCR amplification of a random sequence DNA library by DMSO and betaine: application to in vitro combinatorial selection of aptamers. J Biochem Biophys Methods 2005;64(2):147-51
  • Giambernardi TA, Rodeck U, Klebe RJ. Bovine serum albumin reverses inhibition of RT-PCR by melanin. Biotechniques 1998;25(4):564-6
  • Nagai M, Yoshida A, Sato N. Additive effects of bovine serum albumin, dithiothreitol, and glycerol on PCR. Biochem Mol Biol Int 1998;44(1):157-63
  • Svec D, Andersson D, Pekny M, et al. Direct cell lysis for single-cell gene expression profiling. Front Oncol 2013;3:274
  • Spiess AN, Mueller N, Ivell R. Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of taq polymerase by the disaccharide trehalose. Clin Chem 2004;50(7):1256-9
  • Zhang Z, Kermekchiev MB, Barnes WM. Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq. J Mol Diagnost 2010;12(2):152-61
  • Bookstein R, Lai CC, To H, Lee WH. PCR-based detection of a polymorphic BamHI site in intron 1 of the human retinoblastoma (RB) gene. Nucleic Acids Res 1990;18(6):1666
  • Sarkar G, Kapelner S, Sommer SS. Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res 1990;18(24):7465
  • Ohler LD, Rose EA. Optimization of long-distance PCR using a transposon-based model system. PCR Methods Appl 1992;2(1):51-9
  • Sachdeva R, Simm M. Application of linear polyacrylamide coprecipitation of denatured templates for PCR amplification of ultra-rapidly reannealing DNA. Biotechniques 2011;50(4):217-19
  • Cheng S, Fockler C, Barnes WM, Higuchi R. Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci USA 1994;91(12):5695-9
  • Fortier ME, Kent S, Ashdown H, et al. The viral mimic, polyinosinic:polycytidylic acid, induces fever in rats via an interleukin-1-dependent mechanism. Am J Physiol 2004;287(4):R759-66
  • Chevet E, Lemaitre G, Katinka MD. Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res 1995;23(16):3343-4
  • Kovarova M, Draber P. New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res 2000;28(13):E70
  • Melchior WBJr, Von Hippel PH. Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. Proc Natl Acad Sci USA 1973;70(2):298-302
  • George S, Sokolenko S, Aucoin MG. Rapid and cost-effective baculovirus sample preparation method as a viable alternative to conventional preparation for quantitative real-time PCR. J Virolog Methods 2012;182;1-2:27-36
  • Peper G, Fankhauser A, Merlin T, et al. Direct real-time quantitative PCR for measurement of host-cell residual DNA in therapeutic proteins. J Pharmaceut Biomed Anal 2014;100:123-30
  • Wang QT, Xiao W, Mindrinos M, Davis RW. Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling. BioTechniques 2002;33(4): 788, 790, 792 passim