Searching journal content for articles similar to Jung et al. 1 (3): 171.

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  1. Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
    • Yanjun Zhang,
    • Yin Tang,
    • Zhongxing Sun,
    • Junqi Jia,
    • Yuan Fang,
    • Xinyi Wan,
    • and Dong Fang
    Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
    ...et al. 2021). To explore how Tn5 tagments different nucleic acid substrates, we treated double-stranded DNA (dsDNA), total RNA, and ssDNA with the Tn5 transposon.As previously reported (Naumann and Reznikoff 2002), Tn5 transposon tagmented dsDNA, which was purified as genomic DNA from HEK293T cells...
  2. REVIEW: Sequencing of PCR-amplified DNA.
    • I S Bevan,
    • R Rapley,
    • and M R Walker
    Genome Res. May 1992 1: 222-228; doi:10.1101/gr.1.4.222
    ...differences, in all situations the purity and concentration of PCR-amplified DNA template used remains the most critical factor determining the efficiency and reliability of nucleotide sequencing methods. Footnotes Copyright © Cold Spring Harbor Laboratory Press Bevan, I S Bevan I S Walker...
  3. Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
    • Xiaoyang Dou,
    • Jerome D. Boyd-Kirkup,
    • Joseph McDermott,
    • Xiaoli Zhang,
    • Fang Li,
    • Bowen Rong,
    • Rui Zhang,
    • Bisi Miao,
    • Peilin Chen,
    • Hao Cheng,
    • Jianhuang Xue,
    • David Bennett,
    • Jiemin Wong,
    • Fei Lan,
    • and Jing-Dong J. Han
    Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
    ...cells (Fig. 2C). Unmethylated lambda DNA was used as a spike-in control, and two PCR products of mtDNA were used as an unmethylated mtDNA negative control to ensure bisulfite conversion efficiency (Fig. 2D). Sequences were strand-specifically mapped (Supplemental Information) and analyzed to ensure all...
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  4. METHODS: Efficient High-Throughput Resequencing of Genomic DNA
    • Raymond D. Miller,
    • Shenghui Duan,
    • Elizabeth G. Lovins,
    • Ellen F. Kloss,
    • and Pui-Yan Kwok
    Genome Res. April 1, 2003 13: 717-720; Published in Advance March 12, 2003, doi:10.1101/gr.886203
    ...containing 1.42 million single nucleotide polymorphisms. Nature 409 : 928 – 933 . ↵ Kaltenboeck B. , Spatafora J.W. , Zhang X. , Kousoulas K.G. , Blackwell M. , Storz J. ( 1992 ) Efficient production of single-stranded DNA as long as 2 kb for sequencing of PCR-amplified DNA. Biotechniques 12 : 164 – 171...
  5. Method: Extending the spectrum of DNA sequences retrieved from ancient bones and teeth
    • Isabelle Glocke and
    • Matthias Meyer
    Genome Res. July 2017 27: 1230-1237; Published in Advance April 13, 2017, doi:10.1101/gr.219675.116
    ...: single strand or double strand? Biotechniques 56: 289–300. Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prufer K, Meyer M, Krause J, RonanMT, LachmannM, et al. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci 104: 14616–14621. Glocke and Meyer 1236 Genome...
  6. REVIEW: Pyrosequencing Sheds Light on DNA Sequencing
    • Mostafa Ronaghi
    Genome Res. January 1, 2001 11: 3-11; doi:10.1101/gr.150601
    ...was developed for sequencing on double-stranded DNA template ( Nordstrom et al. 2000a , b ). This template preparation method employs a nucleotide-degrading enzyme and exonuclease I. The enzymes are added to the PCR product and the mixture is incubated at room temperature or 35°C. During this step...
  7. Next-Generation DNA Sequencing/Review: The new paradigm of flow cell sequencing
    • Robert A. Holt and
    • Steven J.M. Jones
    Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107
    ...templates from complex mixtures extend the utility of these platforms for genome analysis. Given the ever increasing demand for DNA sequence information, we can expect continuous improvement of this new generation of instruments and their eventual replacement by even more powerful technology. Footnotes...
  8. REVIEW: PCR, direct sequencing, and the comparative approach.
    • T D Kocher
    Genome Res. May 1992 1: 217-221; doi:10.1101/gr.1.4.217
    .... 5. Murray, V. Murray, V. 1989 . Improved double-stranded DNA sequencing using the linear polymerase chain reaction. Nucleic Acids Res. 17 : 8889 . 6. Thomas, W.K. , Kocher. T.D. Thomas, W.K. and Kocher. T.D. 1992 . Sequencing of PCR-amplified DNAs. Methods Enzymol. (in press). 7. Ferl, R.J., C...
  9. Method: Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases
    • Tony Gutschner,
    • Marion Baas,
    • and Sven Diederichs
    Genome Res. November 2011 21: 1944-1954; Published in Advance August 15, 2011, doi:10.1101/gr.122358.111
    ...–6822 of mMALAT1 (GenBank: NR_002847.2) were PCR amplified from genomic DNA of murine embryonic fibroblasts. A list of all cloning Gutschner et al. 1952 Genome Research www..org primers can be found in Supplemental Table 3. The sequences contain a random overhang for restriction enzyme binding...
  10. Method: High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
    • Sam Alsford,
    • Daniel J. Turner,
    • Samson O. Obado,
    • Alejandro Sanchez-Flores,
    • Lucy Glover,
    • Matthew Berriman,
    • Christiane Hertz-Fowler,
    • and David Horn
    Genome Res. June 2011 21: 915-924; Published in Advance March 1, 2011, doi:10.1101/gr.115089.110
    ...biology of Trypanosoma brucei differentiation. Curr Opin Microbiol 10: 539–546. Field MC, Carrington M. 2009. The trypanosome flagellar pocket. Nat Rev Microbiol 7: 775–786. Glover L, Horn D. 2009. Site-specific DNA double-strand breaks greatly increase stable transformation efficiency in Trypanosoma...
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