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REVIEW: Advanced methods in PCR product detection.
- J G Lazar
Genome Res. August 1994 4: S1-S14
...products. Mol Cell Probes 6 : 245 – 249 . 10. He, Y., Coutlee, F. Saint-Antoine, P. Oliver, C. Voyer, H. and Kesous-Elbaz. A. 1993 . Detection of polymerase chain reaction-amplified human immunodeficiency virus type 1 proviral DNA with a digoxigenin-labeled RNA probe and an enzyme-linked immunoassay. J...
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ARTICLE: Quantitative RNA and DNA gene amplification can rapidly monitor HIV infection and antiviral activity in cell cultures.
- M A Winters,
- M Holodniy,
- D A Katzenstein,
- and T C Merigan
Genome Res. May 1992 1: 257-262; doi:10.1101/gr.1.4.257
.... Keller, H.H., , Huang, D.P. , Manak. M.M. Keller, H.H., Huang, D.P. and Manak. M.M. 1991 . Detection of human immunodeficiency virus type 1 DNA by polymerase chain reaction amplification and capture hybridization in microtiter wells. J. Clin. Microbiol. 29 : 638 – 641 . 20. Mitsuya, H., , Yarchoan, R...
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Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
...alteration based on Xdrop-LRS are shown for each clone. (E) The dot plot shows the quantification cycle (Cq) using genomic template DNA from the HAP1 control clone at increasing concentrations. Both the one-color (circle) and the two-color (triangle) system were tested in the two TaqMan assays, detecting...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...ChIP. Briefly, each cell line clone was crosslinked by paraformaldehyde to lock interacting 21 chromatins in physical contact. Chromatin was digested by a restriction enzyme NlaIII and circularized by T4 22 ligase. NlaIII recognizes and digests 4 base pairs of DNA (CATG), creating a high resolution digestion...
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RESOURCE: Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
...which regions correspond to potential transcripts. Common strategies to this end include aligning the to cDNA sequences, such as the Riken mouse cDNA library ( The FANTOM Consortium and the RIKEN Exploration Research Group Phase I and II 2002 ); the detection of similarity between imputed translations...
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Methods: A novel, high-performance random array platform for quantitative gene expression profiling
- Kenneth Kuhn,
- Shawn C. Baker,
- Eugene Chudin,
- Minh-Ha Lieu,
- Steffen Oeser,
- Holly Bennett,
- Philippe Rigault,
- David Barker,
- Timothy K. McDaniel,
- and Mark S. Chee
Genome Res. November 2004 14: 2347-2356; doi:10.1101/gr.2739104
...), by which messenger RNA is converted to cDNA, followed by an amplification/labeling step mediated by T7 DNA polymerase. The linear amplification step reduces the amount of starting material needed. We adapted the protocol to a microtiter plate format in order to match the array matrix format, which permits...

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