{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T05:39:36Z","timestamp":1791351576322,"version":"4.3.1"},"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2019,2,22]],"date-time":"2019-02-22T00:00:00Z","timestamp":1550793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["5R33CA183688-02"],"award-info":[{"award-number":["5R33CA183688-02"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["1R43ES024107-01"],"award-info":[{"award-number":["1R43ES024107-01"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["2R44ES24107-02"],"award-info":[{"award-number":["2R44ES24107-02"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0212031","type":"journal-article","created":{"date-parts":[[2019,2,22]],"date-time":"2019-02-22T13:51:35Z","timestamp":1550843495000},"page":"e0212031","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":42,"title":["Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5535-3725","authenticated-orcid":true,"given":"Christy L.","family":"Trejo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4040-0370","authenticated-orcid":true,"given":"Milo\u0161","family":"Babi\u0107","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elliot","family":"Imler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Migdalia","family":"Gonzalez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei I.","family":"Bibikov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Shepard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harper C.","family":"VanSteenhouse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8500-0442","authenticated-orcid":true,"given":"Joanne M.","family":"Yeakley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1342-801X","authenticated-orcid":true,"given":"Bruce E.","family":"Seligmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,2,22]]},"reference":[{"issue":"1","key":"ref1","doi-asserted-by":"crossref","first-page":"e0170632","DOI":"10.1371\/journal.pone.0170632","article-title":"A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples","volume":"12","author":"A Esteve-Codina","year":"2017","journal-title":"PLoS One"},{"issue":"5","key":"ref2","doi-asserted-by":"crossref","DOI":"10.3390\/ijms17050724","article-title":"A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay","volume":"17","author":"F L\u00fcder Ripoli","year":"2016","journal-title":"Int J Mol Sci"},{"issue":"7","key":"ref3","doi-asserted-by":"crossref","first-page":"e70714","DOI":"10.1371\/journal.pone.0070714","article-title":"Quality Control of RNA Preservation and Extraction from Paraffin-Embedded Tissue: Implications for RT-PCR and Microarray Analysis","volume":"8","author":"K Kashofer","year":"2013","journal-title":"PLoS One"},{"issue":"12","key":"ref4","doi-asserted-by":"crossref","first-page":"e1261","DOI":"10.1371\/journal.pone.0001261","article-title":"Determinants of RNA Quality from FFPE Samples","volume":"2","author":"S von Ahlfen","year":"2007","journal-title":"PLoS One"},{"issue":"3","key":"ref5","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1097\/01.pai.0000213119.81343.7b","article-title":"Real-time PCR analysis of RNA extracted from formalin-fixed and paraffin-embeded tissues: effects of the fixation on outcome reliability","volume":"15","author":"F Castiglione","year":"2007","journal-title":"Appl Immunohistochem Mol Morphol"},{"issue":"5","key":"ref6","doi-asserted-by":"crossref","first-page":"e98187","DOI":"10.1371\/journal.pone.0098187","article-title":"Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue","volume":"9","author":"J Hedegaard","year":"2014","journal-title":"PLoS One"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"e0178302","DOI":"10.1371\/journal.pone.0178302","article-title":"A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling","volume":"12","author":"JM Yeakley","year":"2017","journal-title":"PLoS One"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"4407","DOI":"10.1039\/C6GC01147K","article-title":"Chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives","volume":"18","author":"FA Grimm","year":"2016","journal-title":"Green Chem"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/toxsci\/kfx153","article-title":"Genomic effects of androstenedione and sex-specific liver cancer susceptibility in mice","volume":"160","author":"JP Rooney","year":"2017","journal-title":"Toxicol. Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"168","DOI":"10.3389\/fgene.2017.00168","article-title":"A pipeline for high throughput concentration response modeling of gene expression for toxicogenomics","volume":"8","author":"JS House","year":"2017","journal-title":"Front. Genet"},{"key":"ref11","article-title":"A human population-based organotypic in vitro model for cardiotoxicity screening","author":"FA Grimm","year":"2018","journal-title":"ALTEX"},{"issue":"12","key":"ref12","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"10","key":"ref13","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":"S Anders","year":"2010","journal-title":"Genome Biol"},{"issue":"6","key":"ref14","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"GTEx Consortium","year":"2013","journal-title":"Nat Genet"},{"issue":"2","key":"ref15","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1074\/mcp.M113.035600","article-title":"Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics","volume":"13","author":"L Fagerberg","year":"2014","journal-title":"Mol Cell Proteomics"},{"issue":"3","key":"ref16","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.bbrc.2005.03.046","article-title":"Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells","volume":"330","author":"T Itoh","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"issue":"5","key":"ref17","doi-asserted-by":"crossref","first-page":"239","DOI":"10.2144\/000114415","article-title":"The paraffin-embedded RNA metric (PERM) for RNA isolated from formalin-fixed, paraffin-embedded tissue","volume":"60","author":"JY Chung","year":"2016","journal-title":"Biotechniques"},{"issue":"9","key":"ref18","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1097\/01.MP.0000026054.62220.FC","article-title":"Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses","volume":"15","author":"M Macabeo-Ong","year":"2002","journal-title":"Mod Pathol"},{"issue":"1","key":"ref19","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0002-9440(10)63093-3","article-title":"Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay","volume":"164","author":"M Cronin","year":"2004","journal-title":"Am J Pathol"},{"issue":"9","key":"ref20","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/nbt.2957","article-title":"A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium","volume":"32","year":"2014","journal-title":"Nat Biotechnol"},{"key":"ref21","unstructured":"Illumina White Paper: Sequencing, Pub. No. 470-2011-004, 12 April 2011"},{"issue":"5","key":"ref22","doi-asserted-by":"crossref","first-page":"e0197162","DOI":"10.1371\/journal.pone.0197162","article-title":"A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells","volume":"13","author":"A Wolff","year":"2018","journal-title":"PLoS One"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-4939-1050-2_3","article-title":"Tissue processing and hematoxylin and eosin staining","volume":"1180","author":"AT Feldman","year":"2014","journal-title":"Methods Mol Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0212031","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T11:22:20Z","timestamp":1589023340000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0212031"}},"subtitle":[],"editor":[{"given":"Francisco X.","family":"Real","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,22]]},"references-count":23,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2019,2,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0212031","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/412015","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,22]]}}}