{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T14:26:27Z","timestamp":1786112787032,"version":"build-2736575974"},"reference-count":25,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T00:00:00Z","timestamp":1776038400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["12A6F26N"],"award-info":[{"award-number":["12A6F26N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["11H7523N"],"award-info":[{"award-number":["11H7523N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["11C1623N"],"award-info":[{"award-number":["11C1623N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["1266325N"],"award-info":[{"award-number":["1266325N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005026","name":"Foundation Against Cancer","doi-asserted-by":"publisher","award":["2025-085"],"award-info":[{"award-number":["2025-085"]}],"id":[{"id":"10.13039\/501100005026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019781","name":"Universitair Ziekenhuis Antwerpen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007660","name":"Universiteit Antwerpen","doi-asserted-by":"publisher","award":["52065"],"award-info":[{"award-number":["52065"]}],"id":[{"id":"10.13039\/501100007660","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011878","name":"Vlaamse regering","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011878","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006282","name":"King Baudouin Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006282","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100021906","name":"Vermont Studio Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100021906","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019618","name":"Vlaams Supercomputer Centrum","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019618","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004385","name":"Ghent University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004385","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011851","name":"Kom op tegen kanker","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011851","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.xpro.2026.104540","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T15:09:56Z","timestamp":1779116996000},"page":"104540","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol for total RNA sequencing analysis of extracellular RNA from biofluids"],"prefix":"10.1016","volume":"7","author":[{"given":"Anneleen","family":"Decock","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly","family":"Verniers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Decruyenaere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1791-2359","authenticated-orcid":false,"given":"Annelien","family":"Morlion","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasper","family":"Verwilt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2026.104540_bib1","doi-asserted-by":"crossref","DOI":"10.3389\/fonc.2023.1221471","article-title":"Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies","volume":"13","author":"Decruyenaere","year":"2023","journal-title":"Front. Oncol."},{"key":"10.1016\/j.xpro.2026.104540_bib2","doi-asserted-by":"crossref","first-page":"9982","DOI":"10.3390\/ijms25189982","article-title":"Characterizing the cell-free transcriptome in a humanized diffuse large B-cell lymphoma patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting","volume":"25","author":"Decruyenaere","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.xpro.2026.104540_bib3","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-53892-x","article-title":"Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles","volume":"9","author":"Everaert","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.xpro.2026.104540_bib4","doi-asserted-by":"crossref","first-page":"zcac037","DOI":"10.1093\/narcan\/zcac037","article-title":"Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA","volume":"4","author":"Vermeirssen","year":"2022","journal-title":"NAR Cancer"},{"key":"10.1016\/j.xpro.2026.104540_bib5","first-page":"7","article-title":"Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma","volume":"2","author":"Deleu","year":"2023","journal-title":"ExRNA"},{"key":"10.1016\/j.xpro.2026.104540_bib6","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1080\/15476286.2021.1971438","article-title":"Custom long non-coding RNA capture enhances detection sensitivity in different human sample types","volume":"18","author":"Morlion","year":"2021","journal-title":"RNA Biol."},{"key":"10.1016\/j.xpro.2026.104540_bib7","doi-asserted-by":"crossref","first-page":"4513","DOI":"10.1038\/s41467-025-58607-7","article-title":"Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling","volume":"16","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xpro.2026.104540_bib8","doi-asserted-by":"crossref","first-page":"2679","DOI":"10.1111\/jth.15867","article-title":"Removal of platelets from blood plasma to improve the quality of extracellular vesicle research","volume":"20","author":"Bettin","year":"2022","journal-title":"J. Thromb. Haemostasis"},{"key":"10.1016\/j.xpro.2026.104540_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108552","article-title":"Charting extracellular transcriptomes in the human biofluid RNA atlas","volume":"33","author":"Hulstaert","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.xpro.2026.104540_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2021.100475","article-title":"Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls","volume":"2","author":"Hulstaert","year":"2021","journal-title":"STAR Protoc."},{"key":"10.1016\/j.xpro.2026.104540_bib11","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/nmeth.3957","article-title":"Representing genetic variation with synthetic DNA standards","volume":"13","author":"Deveson","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104540_bib12","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1038\/nmeth.3958","article-title":"Spliced synthetic genes as internal controls in RNA sequencing experiments","volume":"13","author":"Hardwick","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104540_bib13","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.xpro.2026.104540_bib14","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2026.104540_bib15","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"10.1016\/j.xpro.2026.104540_bib16","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq - A Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2026.104540_bib17","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","article-title":"RSeQC: quality control of RNA-seq experiments","volume":"28","author":"Wang","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2026.104540_bib18","author":"Andrews"},{"key":"10.1016\/j.xpro.2026.104540_bib19","series-title":"R: A Language and Environment for Statistical Computing","year":"2025"},{"key":"10.1016\/j.xpro.2026.104540_bib20","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.xpro.2026.104540_bib21","author":"Xie"},{"key":"10.1016\/j.xpro.2026.104540_bib22","series-title":"Collaborative Data Science","year":"2015"},{"key":"10.1016\/j.xpro.2026.104540_bib23","doi-asserted-by":"crossref","first-page":"18934","DOI":"10.1073\/pnas.2001675117","article-title":"When DNA gets in the way: A cautionary note for DNA contamination in extracellular RNA-seq studies","volume":"117","author":"Verwilt","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2026.104540_bib25","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1038\/nmeth.3014","article-title":"Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study","volume":"11","author":"Mestdagh","year":"2014","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104540_bib26","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1038\/s41592-023-01944-6","article-title":"Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision","volume":"20","author":"Vromman","year":"2023","journal-title":"Nat. Methods"}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726001930?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726001930?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T15:48:29Z","timestamp":1785944909000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166726001930"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":25,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S2666166726001930"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104540","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for total RNA sequencing analysis of extracellular RNA from biofluids","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104540","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104540"}}