Searching journal content for articles similar to Kawaji et al. 24 (4): 708.

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  1. Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
    • Ju Heon Maeng,
    • H. Josh Jang,
    • Alan Y. Du,
    • Shin-Cheng Tzeng,
    • and Ting Wang
    Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
    ...concordant with TSS peaks called by RAMPAGE, CAGE-seq, and GRO-cap signals using human cancer cell lines. In addition, robust long-read full-length RNA-seq has the advantage of trivially identifying alternative transcripts. Previous studies have also shown that long-read sequencing can identify thousands...
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  2. Method: End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data
    • Alan Derr,
    • Chaoxing Yang,
    • Rapolas Zilionis,
    • Alexey Sergushichev,
    • David M. Blodgett,
    • Sambra Redick,
    • Rita Bortell,
    • Jeremy Luban,
    • David M. Harlan,
    • Sebastian Kadener,
    • Dale L. Greiner,
    • Allon Klein,
    • Maxim N. Artyomov,
    • and Manuel Garber
    Genome Res. October 2016 26: 1397-1410; Published in Advance July 28, 2016, doi:10.1101/gr.207902.116
    ...only a single mate out of the pair to mimic single end-sequencing available in most standard sequencing core facilities. In our analysis, we used one mate read at the 3′ end of each cDNA fragment (5′ end in the original RNA fragment) (Fig. 1A). In 5′ end (ExoCAGE) libraries, this read should match...
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  3. Method: Unamplified cap analysis of gene expression on a single-molecule sequencer
    • Mutsumi Kanamori-Katayama,
    • Masayoshi Itoh,
    • Hideya Kawaji,
    • Timo Lassmann,
    • Shintaro Katayama,
    • Miki Kojima,
    • Nicolas Bertin,
    • Ai Kaiho,
    • Noriko Ninomiya,
    • Carsten O. Daub,
    • Piero Carninci,
    • Alistair R.R. Forrest,
    • and Yoshihide Hayashizaki
    Genome Res. July 2011 21: 1150-1159; Published in Advance May 19, 2011, doi:10.1101/gr.115469.110
    ...to a plethora of short read methods to profile the transcriptional output of the . RNA-seq (shotgun transcriptome sequencing), digital gene expression (DGE), short RNA libraries, and cap analysis of gene expression (CAGE) have all been adapted to the current high-throughput, short read, second...
  4. Method: High-confidence coding and noncoding transcriptome maps
    • Bo-Hyun You,
    • Sang-Ho Yoon,
    • and Jin-Wu Nam
    Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
    ...) and poly(A) position profiling followed by sequencing (3Pseq) (Ulitsky et al. 2011; Nam and Bartel 2012), have been successfully applied to define the ends of transcripts at single-base resolution. Integrative analysis of the specialized RNA-seq data including CAGE-seq and poly(A)-seq enabled...
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  5. 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
    ...values for pairwise comparisons between TMM-normalized per-gene STRIPE-seq and poly(A)+ RNA-seq fragment counts.Systematic comparison of yeast STRIPE-seq with CAGE-based methodsA previous study used three distinct iterations of CAGE (nanoCAGE, nAnT-iCAGE, and SLIC-CAGE) (Cvetesic et al. 2018) to profile...
  6. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...variants in regulatory sequences. – Conservation of regulatory mechanisms in GOI orthologs in other organisms. Identifying regulatory regionsTo determine TSS(s) by data mining, whole- 5′-RACE, CAGE, or RNA-seq experiments are readily available either through browsers or through dedicated databases like...
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