{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T22:27:28Z","timestamp":1791930448649,"version":"4.3.4"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018502","name":"Kanazawa University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018502","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>RNA sequencing (RNA-seq) technologies enable comprehensive transcriptomic profiling, yet systematic comparisons using identical biological samples remain limited. Here, we performed a multi-faceted comparison of long-read (PacBio) and short-read (Illumina) RNA-seq using the same RNA from peripheral blood cells of four healthy donors. Unlike prior studies that aggregate datasets from different sources, this study evaluates platform-dependent performance across gene expression, transcript variants, fusion genes, primary microRNAs (pri-miRNAs), and immune receptor complementarity-determining region 3 (CDR3) regions using widely available software, highlighting both reproducibility and accessibility. Long-read sequencing outperformed short-read sequencing in detecting complex alternative splicing events, novel transcript isoforms, and full-length immune receptor sequences, particularly immunoglobulin heavy chains, enhancing clonotype resolution. Both platforms captured largely overlapping pri-miRNAs and CDR3 sequences, but each also detected unique elements, demonstrating that total RNA can serve as a proxy for these specialized features when dedicated kits are not used. Short-read sequencing retained superior quantification accuracy for highly expressed genes and stronger concordance with microarray data. Collectively, our findings reveal the complementary strengths of long- and short-read RNA-seq and provide a practical framework for systematic, side-by-side comparison of transcriptomic features, emphasizing the benefits of using the same input material and standard analysis pipelines.<\/jats:p>","DOI":"10.1093\/narmme\/ugag006","type":"journal-article","created":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T12:21:34Z","timestamp":1768825294000},"source":"Crossref","is-referenced-by-count":5,"title":["Systematic evaluation of long- and short-read RNA-seq for human peripheral blood"],"prefix":"10.1093","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0434-3054","authenticated-orcid":false,"given":"Sadahiro","family":"Iwabuchi","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University , Kanazawa-shi , Ishikawa 920-8640 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Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University , Kanazawa-shi , Ishikawa 920-8640 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taka-Aki","family":"Sato","sequence":"additional","affiliation":[{"name":"iLAC Co. , Ltd, Tsukuba-shi , Ibaraki 305-8550 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Urabe","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Public Central Hospital of Matto , Hakusan-shi , Ishikawa 924-8588 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4393-3244","authenticated-orcid":false,"given":"Toshinari","family":"Takamura","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University , Kanazawa-shi , Ishikawa 920-8640 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