{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:38:48Z","timestamp":1790761128897,"version":"4.1.0"},"reference-count":36,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2019,2,21]],"date-time":"2019-02-21T00:00:00Z","timestamp":1550707200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["NICHD"],"award-info":[{"award-number":["NICHD"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["ZIA\u2010HD000711"],"award-info":[{"award-number":["ZIA\u2010HD000711"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["currentprotocols.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["CP Neuroscience"],"published-print":{"date-parts":[[2019,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Fluorescent detection of transcripts using RNAscope has quickly become a standard <jats:italic>in situ<\/jats:italic> hybridization (ISH) approach in neuroscience with over 400 publications since its introduction in 2012. RNAscope's sensitivity and specificity allow the simultaneously detection of up to three low abundance mRNAs in single cells (i.e., multiplexing) and, in contrast to other ISH techniques, RNAscope is performed in 1 day. BaseScope, a newer ultrasensitive platform, uses improved amplification chemistry of single oligonucleotide probe pairs (\u223c50 bases). This technique allows discrimination of single nucleotide polymorphisms or splice variants that differ by short exons. A present limitation of BaseScope is that expression analysis is limited to a single gene (i.e., single\u2010plexing). This article outlines detailed protocols for both RNAscope and BaseScope in neuronal tissue. We discuss how to perform ISH experiments using either fresh\u2010frozen or formalin\u2010fixed paraffin\u2010embedded sections, as well as dissociated cultured neurons. We also outline how to obtain quantitative data from hybridized tissue sections. \u00a9 2019 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/cpns.63","type":"journal-article","created":{"date-parts":[[2019,2,21]],"date-time":"2019-02-21T18:47:14Z","timestamp":1550774834000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Detection and Quantification of Multiple RNA Sequences Using Emerging Ultrasensitive Fluorescent <i>In Situ<\/i> Hybridization Techniques"],"prefix":"10.1002","volume":"87","author":[{"given":"Larissa","family":"Erben","sequence":"first","affiliation":[{"name":"Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health  Bethesda Maryland"},{"name":"Institute of Molecular Psychiatry, University of Bonn  Bonn Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andres","family":"Buonanno","sequence":"additional","affiliation":[{"name":"Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,2,21]]},"reference":[{"key":"e_1_2_11_2_1_1","first-page":"e58097","article-title":"Visualizing genetic variants, short targets, and point mutations in the morphological tissue context with an RNA in situ hybridization assay","volume":"138","author":"Anderson C. 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(2012). See above."},{"key":"e_1_2_11_3_3_1","unstructured":"First publication introducing the RNAscope multiplex fluorescent in situ hybridization assay and describes in detail the technology and principles of RNAscope."},{"key":"e_1_2_11_3_4_1","unstructured":"Bakeret\u00a0al. (2017) Erbenet\u00a0al. (2018) Zhuet\u00a0al. (2018). See above."},{"key":"e_1_2_11_3_5_1","unstructured":"First publications to implement the BaseScope in situ hybridization assay to detect splice variants and single nucleotide polymorphisms and describe its principles as well as validate its sensitivity and specificity."},{"key":"e_1_2_11_4_2_1","unstructured":"https:\/\/acdbio.com"},{"key":"e_1_2_11_4_3_1","unstructured":"Advanced Cell Diagnostics (ACD) the vendor of both RNAscope and BaseScope in situ hybridization assays."},{"key":"e_1_2_11_4_4_1","unstructured":"https:\/\/acdbio.com\/technical\u2010support\/solutions"},{"key":"e_1_2_11_4_5_1","unstructured":"Contains assay overviews and guidelines for scoring and troubleshooting."},{"key":"e_1_2_11_4_6_1","unstructured":"https:\/\/acdbio.com\/science\/applications\/research\u2010solutions\/dual\u2010ish\u2010and\u2010ihc"},{"key":"e_1_2_11_4_7_1","unstructured":"Insights on dual ISH\u2010IHC and data analysis with ImageJ (ACD; TS 46\u2010003)."}],"container-title":["Current Protocols in Neuroscience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fcpns.63","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpns.63","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cpns.63","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpns.63","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,10]],"date-time":"2023-09-10T21:51:42Z","timestamp":1694382702000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpns.63"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,2,21]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,4]]}},"alternative-id":["10.1002\/cpns.63"],"URL":"https:\/\/doi.org\/10.1002\/cpns.63","archive":["Portico"],"relation":{},"ISSN":["1934-8584","1934-8576"],"issn-type":[{"value":"1934-8584","type":"print"},{"value":"1934-8576","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,21]]},"assertion":[{"value":"2019-02-21","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e63"}}