Searching journal content for articles similar to Suzuki et al. 11 (10): 1758.

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  1. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...Sorted B cells in the ASC and MBC gates were separately processed for single-cell RNA-seq using the Chromium Next GEM Single-Cell 3′ Reagent kits v3.1 (10x Genomics) according to the manufacturer instructions with modifications: After the GEM-RT cleanup and full-length cDNA amplification step, 50% of the cDNA...
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  2. Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    • Wenyu Zhang,
    • Anja Guenther,
    • Yuanxiao Gao,
    • Kristian Ullrich,
    • Bruno Huettel,
    • Aftab Ahmad,
    • Lei Duan,
    • Kaizong Wei,
    • and Diethard Tautz
    Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
    ...with hallmarks of both, a 5′ CAP and a poly(A) tail. It has been reported that the TeloPrime Full-Length cDNA Amplification Kit could selectively synthesize cDNA molecules from mRNAs carrying a 5′ CAP, in complement to the standard PacBio cDNA library preparation protocol that could only selectively synthesize cDNA...
  3. Method: Quantifying full-length circular RNAs in cancer
    • Ken Hung-On Yu,
    • Christina Huan Shi,
    • Bo Wang,
    • Savio Ho-Chit Chow,
    • Grace Tin-Yun Chung,
    • Raymond Wai-Ming Lung,
    • Ke-En Tan,
    • Yat-Yuen Lim,
    • Anna Chi-Man Tsang,
    • Kwok-Wai Lo,
    • and Kevin Y. Yip
    Genome Res. December 2021 31: 2340-2353; Published in Advance October 18, 2021, doi:10.1101/gr.275348.121
    ...create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels...
  4. Resource: Recent, full-length gene retrocopies are common in canids
    • Kevin Batcher,
    • Scarlett Varney,
    • Daniel York,
    • Matthew Blacksmith,
    • Jeffrey M. Kidd,
    • Robert Rebhun,
    • Peter Dickinson,
    • and Danika Bannasch
    Genome Res. August 2022 32: 1602-1611; Published in Advance August 12, 2022, doi:10.1101/gr.276828.122
    ...assemblies (Supplemental Table S7). We also identified the insertion site for six retroCNVs that had not been resolved through discordant read mapping (Supplemental Table S7). Most of the retroCNVs were full length with respect to the parent genes, with 153/179 (85.5%) containing the entire parental gene...
  5. Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
    • Sarita Poonia,
    • Anurag Goel,
    • Smriti Chawla,
    • Namrata Bhattacharya,
    • Priyadarshini Rai,
    • Yi Fang Lee,
    • Yoon Sim Yap,
    • Jay West,
    • Ali Asgar Bhagat,
    • Juhi Tayal,
    • Anurag Mehta,
    • Gaurav Ahuja,
    • Angshul Majumdar,
    • Naveen Ramalingam,
    • and Debarka Sengupta
    Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
    ...) on the Polaris IFC and single CTO+ & Calcein AM+ & PTPRC− & CD31− cells were selected to capture sites. Finally, single-cell processing was achieved through template-switching mRNA-seq chemistry for full-length cDNA generation and preamplification on IFC. Supplemental Note 5 elaborates the steps involved in m...
  6. Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
    • Nathan P. Roach,
    • Norah Sadowski,
    • Amelia F. Alessi,
    • Winston Timp,
    • James Taylor,
    • and John K. Kim
    Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
    ...used high-throughput cDNA sequencing technologies. For example, in the annotation of the Caenorhabditis elegans transcriptome, more than half of the transcript isoforms lack full-length support and instead rely on inference from short reads that do not span the full length of the isoform. We applied...
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  7. Resource: Gene expression networks in the Drosophila Genetic Reference Panel
    • Logan J. Everett,
    • Wen Huang,
    • Shanshan Zhou,
    • Mary Anna Carbone,
    • Richard F. Lyman,
    • Gunjan H. Arya,
    • Matthew S. Geisz,
    • Junwu Ma,
    • Fabio Morgante,
    • Genevieve St. Armour,
    • Lavanya Turlapati,
    • Robert R.H. Anholt,
    • and Trudy F.C. Mackay
    Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
    ...from 5 µg of total RNA using the Ribo-Zero gold kit (Illumina). Depleted mRNA was fragmented and converted to first-strand cDNA using SuperScript III reverse transcriptase (Invitrogen). During the synthesis of second-strand cDNA, dUTP instead of dTTP was incorporated to label the second-strand cDNA. cDNA...
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  8. RESOURCE: The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes
    • Mark Stapleton,
    • Guochun Liao,
    • Peter Brokstein,
    • Ling Hong,
    • Piero Carninci,
    • Toshiyuki Shiraki,
    • Yoshihide Hayashizaki,
    • Mark Champe,
    • Joanne Pacleb,
    • Ken Wan,
    • Charles Yu,
    • Joe Carlson,
    • Reed George,
    • Susan Celniker,
    • and Gerald M. Rubin
    Genome Res. August 1, 2002 12: 1294-1300; doi:10.1101/gr.269102
    ...The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes Mark Stapleton 1 , 2 , 6 , Guochun Liao 1 , 3 , Peter Brokstein 1 , 3 , Ling Hong 1 , 3 , Piero Carninci 4...
  9. METHODS: Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes
    • Piero Carninci,
    • Yuko Shibata,
    • Norihito Hayatsu,
    • Yuichi Sugahara,
    • Kazuhiro Shibata,
    • Masayoshi Itoh,
    • Hideaki Konno,
    • Yasushi Okazaki,
    • Masami Muramatsu,
    • and Yoshihide Hayashizaki
    Genome Res. October 1, 2000 10: 1617-1630; doi:10.1101/gr.145100
    ...Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes Piero Carninci 1 , Yuko Shibata , Norihito Hayatsu , Yuichi Sugahara , Kazuhiro Shibata , Masayoshi Itoh...
  10. RESOURCE: Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
    • Takeshi Nagashima,
    • Diego G. Silva,
    • Nikolai Petrovsky,
    • Luis A. Socha,
    • Harukazu Suzuki,
    • Rintaro Saito,
    • Takeya Kasukawa,
    • Igor V. Kurochkin,
    • Akihiko Konagaya,
    • and Christian Schönbach
    Genome Res. June 2003 13: 1520-1533; doi:10.1101/gr.1019903
    ...Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS Takeshi Nagashima 1 , 2 , Diego G. Silva 3 , 4 , Nikolai Petrovsky 3 , 4 , Luis A. Socha 3 , 4 , Harukazu Suzuki 5 , Rintaro Saito 5...
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