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RESOURCE: Construction of a BAC Contig Map of Chromosome 16q by Two-Dimensional Overgo Hybridization
- Cliff S. Han,
- Robert D. Sutherland,
- Phillip B. Jewett,
- Mary L. Campbell,
- Linda J. Meincke,
- Judy G. Tesmer,
- Mark O. Mundt,
- John J. Fawcett,
- Ung-Jin Kim,
- Larry L. Deaven,
- and Norman A. Doggett
Genome Res. May 1, 2000 10: 714-721; doi:10.1101/gr.10.5.714
...and characterization of “ chimeric ” yeast artificial chromosome clones by fluorescent in situ suppression hybridization. Genomics 14 : 536 – 541 . ↵ Shizuya H. , Birren B. , Kim U.J. , Mancino V. , Slepak T. , Tachiiri Y. , Simon M. ( 1992 ) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA...
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ARTICLE: Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23
- Anna Antonell,
- Oscar de Luis,
- Xavier Domingo-Roura,
- and Luis Alberto Pérez-Jurado
Genome Res. September 2005 15: 1179-1188; doi:10.1101/gr.3944605
...designed for those amplicons that failed to amplify with the first set (Supplemental Table 3). PCR reactions were set up on a final volume of 10-25 μL including 50-100 ng of genomic DNA, standard reagents, and variable cycling conditions (Supplemental Table 3). Products were visualized on 0.8%-2% agarose...
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LETTER: Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery
- Daniel G. Peterson,
- Stefan R. Schulze,
- Erica B. Sciara,
- Scott A. Lee,
- John E. Bowers,
- Alexander Nagel,
- Ning Jiang,
- Deanne C. Tibbitts,
- Susan R. Wessler,
- and Andrew H. Paterson
Genome Res. May 1, 2002 12: 795-807; Published in Advance April 12, 2002, doi:10.1101/gr.226102
...in the online supplement to this article, www..org ). The 18S-5.8S-26S rDNA locus has been localized by fluorescence in situ hybridization to the longest S. bicolor mitotic metaphase chromosome ( Sang and Liang 2000 ). Likewise, we recently demonstrated that the longest S. bicolor pachytene chromosome...
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Research: Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
...of which are associated with heterochromatin or tandem arrays. We used fluorescence in situ hybridization (FISH) to visualize these tandem arrays, to order and orient sequence contigs within the assembly, and to estimate gap sizes within single-copy regions (Supplemental Figs. S2, S3). Where possible, we...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...by fluorescence in situ hybridization (FISH) in 29 samples from the WGS data set (Supplemental Table S2) and confirmed by segmentation data in this study (Supplemental Fig. S6A). We also identified four SVs involving ALK (Supplemental Fig. S6B); these events were validated via Sanger sequencing (Supplemental Fig...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...locus is shared across the sim-complex but is absent in the outgroup species D. melanogaster, D. erecta, and D. yakuba, suggesting that it arose in the ancestor of the sim-complex. Consistent with our assemblies, we detect fluorescence in situ hybridization signal for 193XP only on the X pericentromere...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...controls. All insets show telomere hybridization exclusively except TARTAHRE, which hybridized to both telomeric and nontelomeric locations (insets designated with an asterisk).To investigate chromosome localization of the newly defined elements, TR2 and TARTAHRE, we conducted either DNA FISH...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...(Vázquez-Diez et al. 2016) to suggest that micronuclei formation is not a consequence of in vitro culture.Previous studies with rhesus macaque embryos using DNA–fluorescent in situ hybridization (DNA-FISH) probes to human Chromosomes (Chr) 13, 16, 18, X, and Y indicated that the incidence of aneuploidy...
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REVIEW: Allelic variation and heterosis in maize: How do two halves make more than a whole?
- Nathan M. Springer and
- Robert M. Stupar
Genome Res. March 2007 17: 264-275; Published in Advance January 25, 2007, doi:10.1101/gr.5347007
...regions, introns, untranslated regions, and single-copy DNA surrounding genes) from multiple strains or varieties in order to identify variation. This variation can then be used for mapping or association studies. An investigation of randomly selected sequences in the maize inbred B73 relative to inbred...
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Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
- Stanislav Volik,
- Benjamin J. Raphael,
- Guiqing Huang,
- Michael R. Stratton,
- Graham Bignel,
- John Murnane,
- John H. Brebner,
- Krystyna Bajsarowicz,
- Pamela L. Paris,
- Quanzhou Tao,
- David Kowbel,
- Anna Lapuk,
- Dmitri A. Shagin,
- Irina A. Shagina,
- Joe W. Gray,
- Jan-Fang Cheng,
- Pieter J. de Jong,
- Pavel Pevzner,
- and Colin Collins
Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
..., and 96 plasmid subclones end sequenced. Plasmids with end sequences mapping to distant genomic loci were identified, and primers straddling the putative breakpoint were designed. In subpanels 1–3, the first lane is DNA from the corresponding BAC clone, the second lane is MCF-7 genomic DNA, the third lane...

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