{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:09:56Z","timestamp":1787026196587,"version":"build-2736575974"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,27]],"date-time":"2023-07-27T00:00:00Z","timestamp":1690416000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["P42ES016465 P30ES030287"],"award-info":[{"award-number":["P42ES016465 P30ES030287"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000139","name":"U.S. Environmental Protection Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000139","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>\n                    <jats:bold>Introduction:<\/jats:bold>\n                    The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (\n                    <jats:italic>Danio rerio<\/jats:italic>\n                    ), respond to toxicant exposure. Recently, the development of 3\u2032 RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3\u2032 RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Methods and results:<\/jats:bold>\n                    Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3\u2032 or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3\u2032 and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Conclusions:<\/jats:bold>\n                    These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3\u2032 RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.\n                  <\/jats:p>","DOI":"10.3389\/fbinf.2023.1234218","type":"journal-article","created":{"date-parts":[[2023,7,27]],"date-time":"2023-07-27T16:59:10Z","timestamp":1690477150000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["3\u2032 RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism"],"prefix":"10.3389","volume":"3","author":[{"given":"Ryan S.","family":"McClure","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Rericha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina M.","family":"Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robyn L.","family":"Tanguay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,27]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/nmeth.2483","article-title":"Comparative analysis of RNA sequencing methods for degraded or low-input samples","volume":"10","author":"Adiconis","year":"2013","journal-title":"Nat. methods"},{"key":"B2","doi-asserted-by":"publisher","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":"B3","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/978-1-4939-9240-9_6","article-title":"Single-cell RNA sequencing with drop-seq","volume":"1979","author":"Bageritz","year":"2019","journal-title":"Methods Mol. 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