{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:51:31Z","timestamp":1753890691716,"version":"3.41.2"},"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><jats:bold>Introduction:<\/jats:bold> 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 (<jats:italic>Danio rerio<\/jats:italic>), 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.<\/jats:p><jats:p><jats:bold>Methods and results:<\/jats:bold> 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.<\/jats:p><jats:p><jats:bold>Conclusions:<\/jats:bold> 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.<\/jats:p>","DOI":"10.3389\/fbinf.2023.1234218","type":"journal-article","created":{"date-parts":[[2023,7,27]],"date-time":"2023-07-27T20:59:10Z","timestamp":1690491550000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"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":[]},{"given":"Yvonne","family":"Rericha","sequence":"additional","affiliation":[]},{"given":"Katrina M.","family":"Waters","sequence":"additional","affiliation":[]},{"given":"Robyn L.","family":"Tanguay","sequence":"additional","affiliation":[]}],"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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