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REVIEW: Multiplex PCR: advantages, development, and applications.
- M C Edwards and
- R A Gibbs
Genome Res. February 1994 3: S65-S75
...to the amplification of rarer target sequences in an otherwise standardized reaction. (12~ Indication of Template Quantity The exponential amplification and internal standards of multiplex PCR can be used to assess the amount of a particular template in a sample. To quan- titate templates accurately by multiplex PCR...
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Research: Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription
- Elizabeth A. Hoffman,
- Andrew McCulley,
- Brian Haarer,
- Remigiusz Arnak,
- and Wenyi Feng
Genome Res. March 2015 25: 402-412; Published in Advance January 21, 2015, doi:10.1101/gr.180497.114
.... 2001). Electrophoresis was conducted for 24 h at 14°C with a switch time ramped from 10 to 90 sec at 6 volts/cm. Standard procedures were used to ethidium bromide stain and photograph the gel. Cloning of AHP1, TSA1, YHK8, and RNR3 PCR products of AHP1, TSA1, YHK8, and RNR3, alongwith flanking sequences...
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Method: Paired-end sequencing of Fosmid libraries by Illumina
- Louise J.S. Williams,
- Diana G. Tabbaa,
- Na Li,
- Aaron M. Berlin,
- Terrance P. Shea,
- Iain MacCallum,
- Michael S. Lawrence,
- Yotam Drier,
- Gad Getz,
- Sarah K. Young,
- David B. Jaffe,
- Chad Nusbaum,
- and Andreas Gnirke
Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
...parallel -sequencing technologies no longer rely on cloning DNA fragments in a bacterial host. The platforms currently on the market (454, Illumina, SOLiD, Ion Torrent) replaced vectors with synthetic adapters and bacterial colonies with PCR-amplified ‘‘clones’’ of DNA fragments tethered to a bead...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...beads. To focus on individual candidate genes predicted to be bound by the protein of interest, precipitated DNA can be analyzed using qPCR with primers designed specifically against the regulatory sequences of the GOIs. Alternatively, in ChIP-seq following precipitation, cross-links are reversed...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
...construction and simply sequence the two ends of DNA fragments using the paired-end sequencing method described above. Although this last approach is simple and straightforward, it is limited to short DNA fragments that can be amplified by bridging PCR on the surface of the flow cells, and therefore, only...
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REPORT: Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7
- James W. Thomas,
- Tyrone J. Summers,
- Shih-Queen Lee-Lin,
- Valerie V. Braden Maduro,
- Jacquelyn R. Idol,
- Stephen D. Mastrian,
- Joseph F. Ryan,
- D. Curtis Jamison,
- and Eric D. Green
Genome Res. May 1, 2000 10: 624-633; doi:10.1101/gr.10.5.624
...then be readily expanded by developing new overgo probes from insert-end sequences of BACs residing at contig ends [e.g., generated by bubble-PCR ( Riley et al. 1990 )] and rescreening the BAC library. Figure 4 depicts a representative example of a SEGMAP -constructed BAC contig spanning &gt;1 Mb of proximal MMU6...
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LETTER: A 7.5 Mb Sequence-Ready PAC Contig and Gene Expression Map of Human Chromosome 11p13–p14.1
- Beate Gawin,
- Alexandra Niederführ,
- Nina Schumacher,
- Holger Hummerich,
- Peter F.R. Little,
- and Manfred Gessler
Genome Res. November 1, 1999 9: 1074-1086; doi:10.1101/gr.9.11.1074
...Niederführ et al. (1998) . End probes of each PAC were generated by linker mediated PCR and hybridized to colony filters of the arrayed sublibrary to identify overlapping clones. Clone insert sizes were determined by Not I restriction digests of the respective PAC clones. Additionally, we used markers...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...–chloroform protocol. Oxford Nanopore native (PCR-free) genomic DNA libraries were prepared in multiplex with kits SQK-LSK109 and EXP-NBD104 (Oxford Nanopore Technologies). Libraries were sequenced with FLO-MIN106 (revC) flowcells on a MinION sequencer (MIN-101B). The sequencing and base-calling were run on a Min...
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Research: Small chromosomal regions position themselves autonomously according to their chromatin class
- Harmen J.G. van de Werken,
- Josien C. Haan,
- Yana Feodorova,
- Dominika Bijos,
- An Weuts,
- Koen Theunis,
- Sjoerd J.B. Holwerda,
- Wouter Meuleman,
- Ludo Pagie,
- Katharina Thanisch,
- Parveen Kumar,
- Heinrich Leonhardt,
- Peter Marynen,
- Bas van Steensel,
- Thierry Voet,
- Wouter de Laat,
- Irina Solovei,
- and Boris Joffe
Genome Res. June 2017 27: 922-933; Published in Advance March 24, 2017, doi:10.1101/gr.213751.116
.... Indeed, gene expression analysis by quantitative PCR for genes present in human and mouse orthologous regions Figure 1. Structural variation of C-HAC and L-HAC. Circos plots show four HAC segments and the structural rearrangements between them. The gene-rich segment is indicated in green; gene-poor, gene...
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Methods: Pooled genomic indexing of rhesus macaque
- Aleksandar Milosavljevic,
- Ronald A. Harris,
- Erica J. Sodergren,
- Andrew R. Jackson,
- Ken J. Kalafus,
- Anne Hodgson,
- Andrew Cree,
- Weilie Dai,
- Miklos Csuros,
- Baoli Zhu,
- Pieter J. de Jong,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. February 2005 15: 292-301; doi:10.1101/gr.3162505
...to BAC mappings, PGI also economically produces closely spaced CASTSs ( Larkin et al. 2003 ). By producing multiple CASTSs per sequencing reaction, PCR-able distances between CASTSs can be achieved much more economically for a by ST-PGI than by other methods. Targeted sequencing of PCR products across...

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