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ARTICLES: Real time quantitative PCR.
- C A Heid,
- J Stevens,
- K J Livak,
- and P M Williams
Genome Res. October 1996 6: 986-994; doi:10.1101/gr.6.10.986
.... Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Applic. 4: 357-362. Livak, K.J., J. Marmaro, and J.A. Todd. 1995b. Towards 994 ~ GENOME RESEARCH fully automated -wide polymorphism screening [Letter...
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METHODS: SNP Genotyping by Multiplexed Solid-Phase Amplification and Fluorescent Minisequencing
- Michael H. Shapero,
- Kerstin K. Leuther,
- Anhthu Nguyen,
- Melissa Scott,
- and Keith W. Jones
Genome Res. November 1, 2001 11: 1926-1934; Published in Advance October 15, 2001, doi:10.1101/gr.205001
...products hybridize to complementary primers that reside in close proximity on the bead surface. After the second extension cycle, double-stranded PCR product is covalently bound to the beads at both of its 5′ ends. During the third and all subsequent denaturation, annealing, and extension cycles...
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ARTICLES: A novel method for real time quantitative RT-PCR.
- U E Gibson,
- C A Heid,
- and P M Williams
Genome Res. October 1996 6: 995-1001; doi:10.1101/gr.6.10.995
.... 1993 . Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Res. 21 : 3761 – 3766 . Livak, K.J., Flood, S.J. Marmaro, J. Giusti, W. and Deetz. K. 1995a . Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR...
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METHODS: DNA Analysis by Fluorescence Quenching Detection
- Ming Xiao and
- Pui-Yan Kwok
Genome Res. May 1, 2003 13: 932-939; doi:10.1101/gr.987803
...amounts (Y molecules each). Because the SNP primers and the dye-terminators are in vast excess over the PCR products, dye-terminator incorporation is linear during initial cycles. As the dye-terminators and SNP primer are being consumed, dye-terminator incorporation becomes nonlinear, and the decrease...
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METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
- Robert G. Blazej,
- Brian M. Paegel,
- and Richard A. Mathies
Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
...: 265 – 271 . ↵ Livak K.J. , Flood S.J.A. , Marmaro J. , Giusti W. , Deetz K. ( 1995 ) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic-acid hybridization. PCR Methods Appl. 4 : 357 – 362 . ↵ Marth G.T. , Korf I...
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GENOME METHODS: A Homogeneous, Ligase-Mediated DNA Diagnostic Test
- Xiangning Chen,
- Kenneth J. Livak,
- and Pui-Yan Kwok
Genome Res. May 1, 1998 8: 549-556; doi:10.1101/gr.8.5.549
...) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Applic. 4 : 357 – 362 . ↵ Livak K.J. , Marmaro J. , Todd J.A. ( 1995b ) Towards fully automated -wide polymorphism screening. Nature Genet. 9 : 341...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...of PROMPTs or depletion of EZH2 should have an effect on the targeted gene expression. To test this hypothesis, we performed RT-qPCR analysis using three strand-specific primer sets: one probing for antisense PROMPTs, one probing for sense promoter pausing–derived RNA, and one probing for sense RNA...
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REVIEW: Reading Bits of Genetic Information: Methods for Single-Nucleotide Polymorphism Analysis
- Ulf Landegren,
- Mats Nilsson,
- and Pui-Yan Kwok
Genome Res. August 1, 1998 8: 769-776; doi:10.1101/gr.8.8.769
...restricted to simultaneously detecting two probes, because FRET requires specific pairs of donor-acceptor dyes, each of which occupies a rather large portion of the visible spectrum. In an alternative homogenous hybridization-based PCR procedure, molecular beacons are used for allele discrimination (Fig. 1 B...
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Methods: Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
- Michael R. Miller,
- Joseph P. Dunham,
- Angel Amores,
- William A. Cresko,
- and Eric A. Johnson
Genome Res. February 2007 17: 240-248; Published in Advance December 22, 2006, doi:10.1101/gr.5681207
...markers. In order to produce an array that types a large number of informative markers, subtractive hybridization is used to enrich for sample-specific RAD tags. RAD-tag clone libraries are generated from these enriched samples. These clone libraries are used as templates for PCR, the products of which...
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METHODS: Determination of Single-Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing
- Anders Alderborn,
- Anna Kristofferson,
- and Ulf Hammerling
Genome Res. August 1, 2000 10: 1249-1258; doi:10.1101/gr.10.8.1249
....J. , Marmaro J. , Giusti W. , Deetz K. ( 1995 ) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridisation. PCR Methods Appl. 4 : 357 – 362 . ↵ Low C.-M. , Yap E.P.-H. , Lee E.J.-D. ( 1998 ) Characterization...

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