Searching journal content for articles similar to Picelli et al. 24 (12): 2033.

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  1. Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    • Maria Grazia Mendoza-Ferri,
    • Gwendoline Lozachmeur,
    • Maximilien Duvina,
    • Laetitia Perret,
    • Didier Merciris,
    • Anne Gigout,
    • and Marco Antonio Mendoza-Parra
    Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
    ...for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ Protein A–transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified...
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  2. Perspective: Tagmentation-based single-cell genomics
    • Andrew C. Adey
    Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
    ...with Epicentre Biotechnologies (Adey et al. 2010).The anatomy of the tagmentation reactionThe first step in tagmentation is the formation of the transposome complexes, composed of a hyperactive variant of the Tn5 transposase homodimer complexed with sequences that contain the 19-bp double-stranded ME sequence...
  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
    ...2003).Tn5 transposases that are assembled with OEs can tagment and transpose OEs into target DNA in vitro; as a result, owing to the tagmentation of Tn5 with specifically designed sequences in OEs, DNA is ready for PCR amplification (Goryshin and Reznikoff 1998; Naumann and Reznikoff 2002). In addition...
  4. Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
    • Qiao Rui Xing,
    • Chadi A El Farran,
    • Ying Ying Zeng,
    • Yao Yi,
    • Tushar Warrier,
    • Pradeep Gautam,
    • James J. Collins,
    • Jian Xu,
    • Peter Dröge,
    • Cheng-Gee Koh,
    • Hu Li,
    • Li-Feng Zhang,
    • and Yuin-Han Loh
    Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
    ...compartments on a Fluidigm C1 microfluidic chip (Fig. 1A). Open chromatin regions of each cell are then tagmented with Tn5 transposase, during which accessible DNA regions (ATAC-DNA) are integrated with sequencing adaptors. Next, mRNA is reverse transcribed to double-stranded cDNA, which is then labeled...
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  5. Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
    • Charles Cole,
    • Ashley Byrne,
    • Matthew Adams,
    • Roger Volden,
    • and Christopher Vollmers
    Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
    ...generated full-length cDNA using a modified first half of the Smart-seq2 protocol (Picelli et al. 2014b). cDNA was then split to generate sequencing libraries with three different methods. First, to generate standard Smart-seq2 libraries, part of this cDNA was tagmented using Tn5 (Picelli et al. 2014a...
  6. Method: ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
    • Tyler J. Hansen and
    • Emily Hodges
    Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
    ...the massive size of the human ; it requires large-scale cloning procedures and produces shallow sequencing coverage of human regulatory elements (Johnson et al. 2018). In addition, STARR-seq assays both accessible and inaccessible chromatin. Thus, many assayed regions are derived from heterochromatin...
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  7. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...in 10 µL of 10 mM Tris-HCl (pH 8.0). The cDNA yield was quantified using a Qubit fluorometer (Invitrogen).Library preparationTo construct the sequencing library, the purified cDNAs were diluted to a concentration of 1 ng/µL and subjected to tagmentation with Tn5A transposase for 10 min at 55°C...
  8. 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
    ...cells. Nat Biotechnol 36: 428–431. doi:10.1038/nbt.4112 ↵Picelli S, Björklund ÅK, Reinius B, Sagasser S, Winberg G, Sandberg R. 2014. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 24: 2033–2040. doi:10.1101/gr.177881.114 ↵Rahbari R, Sheahan T, Modes V...
  9. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ....Libraries were sequenced in a paired-end format on an Illumina NextSeq instrument using NextSeq 500/550 high-output kits (2 × 38 cycles).Tn5 productionTn5 transposase was produced as previously described (Picelli et al. 2014), with the following modifications of the adapter oligos for biotin-ATAC experiments: Tn...
  10. Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
    • Hamish W. King,
    • Nadezda A. Fursova,
    • Neil P. Blackledge,
    • and Robert J. Klose
    Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
    ...in mouse embryonic stem cells: the assay for transposase accessible chromatin (ATAC-seq), DNase I hypersensitivity (DNase-seq), and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq). ATAC-seq and DNase-seq measure accessibility by interrogating the digestion frequency of chromatin by Tn5...
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