Searching journal content for articles similar to Adey 31 (10): 1693.

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  1. Editorial: New frontiers in single-cell genomics
    • Nicholas E. Navin,
    • Orit Rozenblatt-Rosen,
    • and Nancy R. Zhang
    Genome Res. October 2021 31: ix-x; doi:10.1101/gr.276129.121
    ...at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Adey AC. 2021. Tagmentation-based single-cell genomics. Genome Res (this issue) 31: 1693–1705. doi:10.1101/gr.275223.121 ↵Aevermann B, Zhang Y, Novotny M, Keshk M, Bakken T, Miller J, Hodge R, Lelieveldt B, Lein E, Scheuermann RH. 2021...
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  2. Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
    • Howard J. Womersley,
    • Daniel Muliaditan,
    • Ramanuj DasGupta,
    • and Lih Feng Cheow
    Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
    ...contributed equally to this work. Corresponding authors: dasguptar@gis.a-star.edu.sg, bieclf@nus.edu.sgAbstractInterrogating regulatory epigenetic alterations during tumor progression at the resolution of single cells has remained an understudied area of research. Here we developed a highly sensitive single...
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  3. 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
    ...-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA...
  4. Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
    • Roman Spektor,
    • Nathaniel D. Tippens,
    • Claudia A. Mimoso,
    • and Paul D. Soloway
    Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
    ...://creativecommons.org/licenses/by-nc/4.0/.References ↵Adey A, Shendure J. 2012. Ultra-low-input, tagmentation-based whole- bisulfite sequencing. Genome Res 22: 1139–1143. doi:10.1101/gr.136242.111 ↵Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. 2012. methylKit: a comprehensive R package...
  5. Method: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • Simone Picelli,
    • Åsa K. Björklund,
    • Björn Reinius,
    • Sven Sagasser,
    • Gösta Winberg,
    • and Rickard Sandberg
    Genome Res. December 2014 24: 2033-2040; Published in Advance July 30, 2014, doi:10.1101/gr.177881.114
    ...for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from subpicogram amounts of cDNA. The comparison of single-cell RNA...
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  6. Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
    • Robert A. Policastro,
    • R. Taylor Raborn,
    • Volker P. Brendel,
    • and Gabriel E. Zentner
    Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
    ...an adapter sequence to the 5′ end of the cDNA (Zhu et al. 2001). TSS mapping methods incorporating TSRT include 5′ serial analysis of gene expression (5′ SAGE) (Zhang and Dietrich 2005), nano-cap analysis of gene expression (nanoCAGE 2010/2017) (Plessy et al. 2010; Poulain et al. 2017), single-cell tagged...
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