{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T15:20:39Z","timestamp":1773674439144,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources.<\/jats:p>\n                  <jats:p>Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF7, adding more sequencing depth after 10 M reads gives diminishing returns on power to detect DE genes, whereas adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large-scale RNA-seq DE studies. Our analysis showed that sequencing less reads and performing more biological replication is an effective strategy to increase power and accuracy in large-scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies.<\/jats:p>\n                  <jats:p>Availability and implementation: The code used in this paper is provided on: http:\/\/home.uchicago.edu\/\u223cjiezhou\/replication\/. The expression data is deposited in the Gene Expression Omnibus under the accession ID GSE51403.<\/jats:p>\n                  <jats:p>Contact: kpwhite@uchicago.edu<\/jats:p>\n                  <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt688","type":"journal-article","created":{"date-parts":[[2013,12,6]],"date-time":"2013-12-06T20:29:20Z","timestamp":1386361760000},"page":"301-304","source":"Crossref","is-referenced-by-count":429,"title":["RNA-seq differential expression studies: more sequence or more replication?"],"prefix":"10.1093","volume":"30","author":[{"given":"Yuwen","family":"Liu","sequence":"first","affiliation":[{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"},{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"}]},{"given":"Jie","family":"Zhou","sequence":"additional","affiliation":[{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"},{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"}]},{"given":"Kevin P.","family":"White","sequence":"additional","affiliation":[{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"},{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"},{"name":"1 Institute of Genomics and Systems Biology, 2Committee on Development, Regeneration, and Stem Cell Biology and 3Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,12,4]]},"reference":[{"key":"2024111411420848200_btt688-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2024111411420848200_btt688-B2","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1534\/genetics.110.114983","article-title":"Statistical design and analysis of RNA sequencing data","volume":"185","author":"Auer","year":"2010","journal-title":"Genetics"},{"key":"2024111411420848200_btt688-B3","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nature10532","article-title":"The evolution of gene expression levels in mammalian organs","volume":"478","author":"Brawand","year":"2011","journal-title":"Nature"},{"key":"2024111411420848200_btt688-B17","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1093\/bioinformatics\/btt015","article-title":"Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression","volume":"29","author":"Busby","year":"2013","journal-title":"Bioinformatics"},{"key":"2024111411420848200_btt688-B4","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1093\/bib\/bbr004","article-title":"Design and validation issues in RNA-seq experiments","volume":"12","author":"Fang","year":"2011","journal-title":"Brief. 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