{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T11:36:34Z","timestamp":1773660994054,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T00:00:00Z","timestamp":1688083200000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01-GM114864"],"award-info":[{"award-number":["R01-GM114864"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach which is highly accurate at only a small fraction of the cost.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and Caenorhabditis elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of \u223c5%.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Analysis pipeline for this approach is available at GitHub as R package controlFreq (github.com\/gimelbrantlab\/controlFreq).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad254","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T17:57:46Z","timestamp":1684951066000},"page":"i431-i439","source":"Crossref","is-referenced-by-count":5,"title":["Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale"],"prefix":"10.1093","volume":"39","author":[{"given":"Asia","family":"Mendelevich","sequence":"first","affiliation":[{"name":"Altius Institute for Biomedical Sciences , 2211 Elliott Ave , Seattle, WA 98121, United States"}]},{"given":"Saumya","family":"Gupta","sequence":"additional","affiliation":[{"name":"Stem Cell Program, Boston Children\u2019s Hospital , 300 Longwood Avenue , Boston, MA 02115, United States"},{"name":"Department of Stem Cell and Regenerative Biology, Harvard University , 7 Divinity Ave , Cambridge, MA 02138, United States"}]},{"given":"Aleksei","family":"Pakharev","sequence":"additional","affiliation":[]},{"given":"Athanasios","family":"Teodosiadis","sequence":"additional","affiliation":[{"name":"Altius Institute for Biomedical Sciences , 2211 Elliott Ave , Seattle, WA 98121, United States"}]},{"given":"Andrey A","family":"Mironov","sequence":"additional","affiliation":[{"name":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 1-73 Vorobiovy Gory, Lab. Bldg B , Moscow 119992, Russia"},{"name":"Institute of Information Transmission Problems, Russian Academy of Sciences , 19 Bolshoi Karetny per. , Moscow 127994, Russia"}]},{"given":"Alexander A","family":"Gimelbrant","sequence":"additional","affiliation":[{"name":"Altius Institute for Biomedical Sciences , 2211 Elliott Ave , Seattle, WA 98121, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,6,30]]},"reference":[{"key":"2023063008152637900_btad254-B1","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1038\/nmeth.2645","article-title":"Accounting for technical noise in single-cell RNA-seq experiments","volume":"10","author":"Brennecke","year":"2013","journal-title":"Nat Methods"},{"key":"2023063008152637900_btad254-B2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/genetics\/77.1.71","article-title":"The genetics of caenorhabditis 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