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ARTICLE: Spermidine facilitates PCR amplification of target DNA.
- C Y Wan and
- T A Wilkins
Genome Res. December 1993 3: 208-210
.... Contrary to earlier e- ports spurning the use of polyamines in PCR, ~12~ we determined that micromolar concentrations of spermidine nhanced PCR amplif ication significantly from plant DNA and that inclusion of spermi- dine to reactions was vastly superior to the compensatory effects of hot- start PCR...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...targeted genotyping of 45 inversions in 551 individuals by a combination of inverse PCR (iPCR) and multiplex ligation-dependent probe amplification (MLPA) (Giner-Delgado et al. 2019) has increased considerably the available human inversion data, although only IRs up to ∼25–30 kb could be spanned...
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Research: Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance
- Jee Young Chung,
- Qurrat Ul Ain,
- Yoonsung Song,
- Seok-Beom Yong,
- and Yong-Hee Kim
Genome Res. September 2019 29: 1442-1452; Published in Advance August 29, 2019, doi:10.1101/gr.246900.118
...RNAs were extracted and relative mRNA levels were determined by real-time PCR. Fabp4 mRNA was increased in the mature adipocytes (C) as well as both in the epidydimal white adipose tissue (epiWAT) and subcutaneous white adipose tissue (subWAT) of obese mice (D). Phb mRNA levels also increased in (E...
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Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
- Ryan O'Hara,
- Enzo Tedone,
- Andrew Ludlow,
- Ejun Huang,
- Beatrice Arosio,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
...and present hurdles to understanding the roles of mtDNA copy number variation during aging and disease onset and progression. This is at least in part due to the following: (1) the differing PCR amplification efficiency between the mtDNA target and housekeeping genes, leading to altered mtDNA/nDNA ratios...
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Method: Transcript amplification from single bacterium for transcriptome analysis
- Yun Kang,
- Michael H. Norris,
- Jan Zarzycki-Siek,
- William C. Nierman,
- Stuart P. Donachie,
- and Tung T. Hoang
Genome Res. June 2011 21: 925-935; Published in Advance May 2, 2011, doi:10.1101/gr.116103.110
...), elimination of exogenousDNA contaminationwith endonucleases (McrBC and DpnI), and minimization of the reaction volume (10 mL for initial amplification and 100 mL total). All manipulations were performed frombeginning to end in a single tube in a PCR chamber. In addition, this simple method is not labor...
REVIEW: Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR.
- E Fahy,
- D Y Kwoh,
- and T R Gingeras
Genome Res. August 1991 1: 25-33; doi:10.1101/gr.1.1.25
.... Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155 : 335 – 350 . 3. Erlich, H.A., ed. 1989. PCR technology: Principles and amplifications for DNA amplification . Stockton Press, New York. 4. Innis, M.A., D.H. Gelfand, J.J. Sninsky, and T.J. White. 1990. PCR...
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Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
- Nicolae Sapoval,
- Medhat Mahmoud,
- Michael D. Jochum,
- Yunxi Liu,
- R.A. Leo Elworth,
- Qi Wang,
- Dreycey Albin,
- Huw A. Ogilvie,
- Michael D. Lee,
- Sonia Villapol,
- Kyle M. Hernandez,
- Irina Maljkovic Berry,
- Jonathan Foox,
- Afshin Beheshti,
- Krista Ternus,
- Kjersti M. Aagaard,
- David Posada,
- Christopher E. Mason,
- Fritz J. Sedlazeck,
- and Todd J. Treangen
Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
...-CoV-2. In this setting, sensitivity determines how well the detection tests can capture the diversity of all SARS-CoV-2 variants. Lack of sensitivity leads to an increase in false-negative qRT-PCR results, because two or more mismatches can result in increases in CT values and degradation in accuracy...
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Research: A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells
- Keren Imberg-Kazdan,
- Susan Ha,
- Alex Greenfield,
- Christopher S. Poultney,
- Richard Bonneau,
- Susan K. Logan,
- and Michael J. Garabedian
Genome Res. April 2013 23: 581-591; Published in Advance February 12, 2013, doi:10.1101/gr.144774.112
...(Supplemental Table 4) were first generated as dsRNAs from PCR products (received from the NYU RNAi Core Facility). Amplification by PCR was followed by in vitro transcription reactions of the cDNA PCR products into dsRNA using the Ambion MEGAscript T7, T3, and SP6 kits (Life Technologies). The secondary screen...
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Method: Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
- Anand Patel,
- Richard Schwab,
- Yu-Tsueng Liu,
- and Vineet Bafna
Genome Res. February 2014 24: 318-328; Published in Advance December 4, 2013, doi:10.1101/gr.161497.113
...with a simulated annealing algorithm to minimize off-target amplification and maximize efficiency at capturing all possible breakpoints within the target regions. To confirm correct amplification and obtain breakpoints, PCR amplicons are combined without barcoding and simultaneously long-read sequenced using...
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Research: Assessment of palindromes as platforms for DNA amplification in breast cancer
- Jamie Guenthoer,
- Scott J. Diede,
- Hisashi Tanaka,
- Xiaoyu Chai,
- Li Hsu,
- Stephen J. Tapscott,
- and Peggy L. Porter
Genome Res. February 2012 22: 232-245; Published in Advance July 13, 2011, doi:10.1101/gr.117226.110
...cell line, we detected a GAPF-positive region at the centromeric breakpoint of a complex copy-number gain in 8q24.21 that contains the MYC oncogene (Fig. 3A). We next confirmed that the GAPF signal represented a cancer-specific palindrome. A regional PCR-based enrichment analysis following the S1...

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