CINXE.COM

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col-1"> <a href="/image-contest" class="level0">Image Calendar</a> <span class="level0 visible-xs">+</span><div class="menu-content"><div class="container"><div class="row menu__blocks"><div class="col-lg-3 col-md-3 col-sm-3 col-xs-12 menu-col"><div class="sec-title">Image Calendar</div> <span class="sectitle-span">+</span><ul><li><a href="/image-contest">Image Contest</a></li><li><a href="/data-image-gallery">Data Image Gallery</a></li></ul></div></div></div></div></li></ul></div><div class="col-lg-1 col-md-1 col-sm-1 col-xs-12 header-search search__button "><div class="search-icon">Search</div><div class="clear"></div></div></div></div> </header></div><div class="region region-content"><div id="block-system-main" class="block block-system clearfix"><div class="content"><style type="text/css"> .profile .profile-bottom, .profile .profile-content{ max-width: 930px; } </style><div class="page-main-container "><div class="banner-container sticky"> <img class="img-banner" src="https://acdbio.com/sites/default/files/science-banner.jpg"><h2 class="general-title">RNAscope™ Applications</h2></div><div class="content-container container newapplication"><div id="node-104795" class="node node-application" about="/science/applications/research-areas/hiv-siv" typeof="sioc:Item foaf:Document"><div class="nav-tab-container"><ul class="nav nav-tabs page-tabs application-bxslider" id="myTab"><li><a href="/science/applications/research-areas/infectious-diseases">Infectious Diseases</a></li><li><a href="/science/applications/disease-areas/zika-virus-research">Zika Virus</a></li><li class="active"><a href="/science/applications/research-areas/hiv-siv" class="active">HIV & SIV</a></li><li><a href="/science/applications/research-areas/covid-19-coronavirus">COVID-19 Coronavirus</a></li></ul></div><div class="tab-content"><div id="tab0" class="tab-pane fade in active profile"><h1 class="top-profile">HIV/SIV Research</h1><div class="sample-image"><div class="loader-image-gallery"></div><div id="film_roll" class="sample-slider"><div><img src="https://acdbio.com/sites/default/files/styles/film_roll_slider/public/SIV-Non-IsotopicISHcomparedtoRNAscopeISH_0.jpg?itok=qrvElDAh" width="765" height="451" alt="Detection of SIV using non-isotopic ISH compared to the RNAscope ISH (red). Data courtesy of Dr. Jacob Estes of NCI"><p class="slider-below-text"> Detection of SIV using non-isotopic ISH compared to the RNAscope ISH (red). Data courtesy of Dr. Jacob Estes of NCI</p></div><div><img src="https://acdbio.com/sites/default/files/styles/film_roll_slider/public/hiv-siv_0.jpg?itok=GB1ZKArJ" width="765" height="451" alt="Detection of HIV RNA in human CD3+ T cells in the spleen of humanized BLT mice using RNAscope 2.0 HD Reagent Kit-RED. RNAscope ISH was followed by colorimetric immunohistochemistry for human T cells using mAb to human CD3, and nuclei were counterstained "><p class="slider-below-text"> Detection of HIV RNA in human CD3+ T cells in the spleen of humanized BLT mice using RNAscope 2.0 HD Reagent Kit-RED. RNAscope ISH was followed by colorimetric immunohistochemistry for human T cells using mAb to human CD3, and nuclei were counterstained</p></div><div><img src="https://acdbio.com/sites/default/files/styles/film_roll_slider/public/HIV_lung_0.png?itok=_nm6Wr15" width="765" height="451" alt="HIV in human lung tissue"><p class="slider-below-text"> HIV in human lung tissue</p></div></div><style type="text/css"> .loader-image-gallery { position: absolute; left: 0px; top: 0px; width: 100%; height: 100%; z-index: 9999; background: url('/sites/default/files/loading_apple.gif') 50% 35% no-repeat rgb(249,249,249); background-size: 100px; opacity: .8; } .sample-image { position: relative; } </style> <script type="text/javascript"> jQuery(document).ready(function($) { // $('#film_roll').hide(); function preloader(){ $('.loader-image-gallery').hide(); $('#film_roll').show(); } window.onload = preloader; }); </script> </div><div class="profile-content application_node_104795"><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even" property="content:encoded"><p>Despite the success of anti-retroviral therapy (ART), the persistence of HIV reservoirs is a major barrier to overcome before finding a lasting cure. In order to completely eradicate HIV and advance therapeutic interventions, it is important to determine the biological nature of viral latency as well as productively infected cells in tissues including the gastrointestinal tract and those of the lymphatic system. RNAscope™, a highly specific and sensitive <em>in situ</em> hybridization technology, employs a powerful technique to study HIV and SIV in cellular and tissue environments.</p><p><strong>Why use RNAscope™ Assay for HIV and SIV research?</strong></p><ul><li><p><strong>Localize specific cell types and tissues infected with HIV/SIV</strong> – ideal for identifying and measuring persistent reservoirs with single-cell resolution in full morphological context.</p></li><li><p><strong>Detect HIV/SIV RNA sequences despite low or undetectable plasma viral loads with specificity</strong> – with single RNA molecule detection technology, identify individual virus particles and infected cells.</p></li><li><p><strong>Differential detection of viral RNA and proviral DNA</strong> – RNAscope™ probes can be designed to target the sense or antisense sequences to detect the three different configurations of HIV/SIV during the replication cycles:</p><ul><li><p>viral RNA in a virus particle;</p></li><li><p>viral genomic RNA or mRNA in an infected cell;</p></li><li><p>proviral DNA integrated in the nucleus of an infected cell.</p></li></ul></li></ul><p> </p><p>Read Science's news article <a href="http://www.sciencemag.org/news/2015/07/molecular-microscope-finds-hidden-aids-virus-body" style="line-height: 20.8px;">'Molecular microscope' finds hidden AIDS virus in the body"</a> regarding Dr. Jake Estes of the Frederick National Laboratory of the National Cancer Institute and the application of RNAscope™ technology in HIV/SIV research. Dr. Estes and collaborators recently authored the publication <strong><a href="https://www.paijournal.com/index.php/paijournal/article/view/100/43">Defining HIV and SIV Reservoirs in Lymphoid Tissues.</a> </strong>The team of researchers<strong> </strong>outline methodology to visualize viral RNA and viral DNA simultaneously in HIV-1/SIV. <a href="https://acdbio.com/innovations-rnascope">Read more</a></p><div class="spotlights"><div class="researcher-bottom testimonial"><div class="row"><div class="col-md-12"><div class="testimonial-desc"><p>"The identification and anatomic location of HIV-infected cells and the effects of tissue environment on virus replication and viral gene expression are all critical for evaluating the pathogenesis of HIV infection and for developing cure strategies to eliminate HIV reservoirs. RNAscope <em>in situ</em> hybridization (ISH) has enabled us to visualize and quantify HIV RNA with single-copy resolution. For work supported by a Federal Contract with NIAID, NIH, we are using this state-of-the-art ISH technology in combination with immunohistochemistry to characterize the tissue and cellular compartments where the virus resides in HIV-infected humanized mice."</p></div><div class="testimonial-auth"><a href="http://profiles.ucsf.edu/cheryl.stoddart">Dr. Cheryl Stoddart</a> and <a href="http://profiles.ucsf.edu/ekaterina.maidji">Dr. Ekaterina Maidji</a></div><div class="testimonial-role"><p>UCSF School of Medicine. Recent publication citing RNAscope<span style="font-size: 10.83px;"><sup>®</sup></span> assay:J Neurovirol. 2015 Nov 16. <a href="http://www.ncbi.nlm.nih.gov/pubmed/26572785" target="_blank">PMID: 26572785</a>.</p></div></div></div></div></div></div></div></div><div class="view view-application view-id-application view-display-id-block_8 view-dom-id-5cb70303f2daafdfba372f34674c6025"></div><div class="view view-application view-id-application view-display-id-block_9 view-dom-id-88aa6af526832ddf8c7cf735dc1eb999"><div class="view-content"><style type="text/css"> .view-id-application.view-display-id-block_9 .row.immuno-watch { margin-top: 15px; margin-bottom: 15px; } </style></div></div></div><div class="sample-image"><div class="profile-bottom"></div></div><div class="spotlight"><div class="profile-bottom spot"><div class="classification application-table hiv-siv-table"><h2>RNAscope<sup><span style="color: black; font-family: arial,sans-serif; font-size: 10pt;"><sup>®</sup></span></sup> Catalog Probes Targeting HIV: </h2><p>(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )</p><div class="read-more-table"><table><thead><tr><th><p><strong>Target species & region</strong></p></th><th><p><strong>Cat. No & Probe Description</strong></p></th></tr></thead><tbody><tr><td><p>HIV1</p><p>Targeting Env, Gag, Pol genes</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">450141</a>       Probe-V-HIV1-env</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">450151</a>       Probe-V-HIV1-env-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">311921</a>       Probe-V-HIV1 (Gag)</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">446211-C2</a> Probe-V-HIV1-Gag-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317691</a>       Probe-V-HIV1-gagpol</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317701</a>       Probe-V-HIV1-gagpol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317701-C2</a> Probe-V-HIV1-gagpol-sense-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">445651</a>       Probe-V-HIV1-gagpol-sense-scrambled</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">445651-C2</a> Probe-V-HIV1-gagpol-sense-scrambled-C2</p></td></tr><tr><td><p>HIV1,</p><p>Excluding Gag and Pol genes</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317711</a>       Probe-V-HIV1-nongagpol</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317711-C2</a> Probe-V-HIV1-nongagpol-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">453631</a>       Probe-V-HIV1-nongagpol-scrambled</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317721</a>       Probe-V-HIV1-nongagpol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">317721-C3</a> Probe-V-HIV1-nongagpol-sense-C3</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">445661</a>       Probe-V-HIV1-nongagpol-sense-scrambled</p></td></tr><tr><td><p>HIV1,</p><p>Subtype A</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416101</a>       Probe-V-HIV1-CladeA</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">426341</a>       Probe-V-HIV1-CladeA-sense</p></td></tr><tr><td><p>HIV1,</p><p>Subtype B</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416111</a>       Probe-V-HIV1-CladeB</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416111-C2</a> Probe-V-HIV1-CladeB-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444051</a>       Probe-V-HIV1-CladeB-gag-pol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">447711</a>       Probe-V-HIV1-CladeB-scrambled</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">425531</a>       Probe-V-HIV1-CladeB-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">425531-C2</a> Probe-V-HIV1-CladeB-sense-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">425531-C3</a> Probe-V-HIV1-CladeB-sense-C3</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444061-C2</a> Probe-V-HIV1-CladeB-vif-vpr-tat-rev-vpu-env-nef-tar-C2</p></td></tr><tr><td><p>HIV1,</p><p>Subtype C</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">429841</a>       Probe-V-HIV1-CladeC</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444021</a>       Probe-V-HIV1-CladeC-gag-pol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">430171</a>       Probe-V-HIV1-CladeC-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444041-C2</a> Probe-V-HIV1-CladeC-vif-vpr-rev-vpu-env-nef-tar-C2</p></td></tr><tr><td><p>HIV1,</p><p>Subtype D</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416121</a>       Probe-V-HIV1-CladeD</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">426351</a>       Probe-V-HIV1-CladeD-sense</p></td></tr><tr><td><p>HIV1,</p><p>Subtype AE</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">446551</a>       Probe-V-HIV-CladeAE</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444011</a>       Probe-V-HIV1-CladeAE-gag-pol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">444031-C2</a>  Probe-V-HIV1-CladeAE-vif-vpr-tat-rev-vpu-env-nef-tar-C2</p></td></tr><tr><td><p>HIV2</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">446221-C3</a>  Probe-V-HIV2-gag-C3</p></td></tr></tbody></table></div><h2> </h2><h2>RNAscope<sup><span style="color: black; font-family: arial,sans-serif; font-size: 10pt;"><sup>®</sup></span></sup> Catalog Probes Targeting SIV: </h2><p>(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )</p><div class="read-more-table"><table><thead><tr><th><p><strong>Target SIV strain</strong></p></th><th><p><strong>Cat. No & Probe Description</strong></p></th></tr></thead><tbody><tr><td><p>SIV-Mac329</p><p>(rhesus monkey, Macaca mulatta)</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">312811</a>        Probe-SIVmac239</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">312811-C2</a>  Probe-SIVmac239-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">314071</a>        Probe-SIVmac239-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">314071-C2</a>  Probe-SIVmac239-sense-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">314451</a>        Probe-SIVmac239-gag</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">445431</a>        Probe-V-SIVmac239-rev-env</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">445441</a>        Probe-V-SIVmac239-vif-vpr-tat</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416131</a>        Probe-V-SIVmac239-vif-env-nef-tar</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416131-C2</a>  Probe-V-SIVmac239-vif-env-nef-tar-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416141</a>        Probe-V-SIVmac239-gag-pol-sense</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">416141-C2</a>  Probe-V-SIVmac239-gag-pol-sense-C2</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">459071-C3</a>  Probe-V-SIVmac239-vif-env-nef-tar-sense-C3</p></td></tr><tr><td><p>SIV-amg</p><p>(african green monkey, Cercopithecus aethiops)</p></td><td><p><a class="go-to-search" href="#" style="line-height: 20.8px;">431811</a>       Probe-V-SIV-gag</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">431821</a>       Probe-V-SIV-pol</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">431831</a>       Probe-V-SIV-rev-env</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">431841</a>       Probe-V-SIV-vif-vpr-tat</p><p><a class="go-to-search" href="#" style="line-height: 20.8px;">432081</a>       Probe-V-SIV</p></td></tr><tr><td><p>SIV-sm sooty mangabey</p><p>(sooty mangabey, Cercocebus atys)</p></td><td><a class="go-to-search" href="#" style="line-height: 20.8px;">415351</a>       Probe-V-SIVsmm</td></tr></tbody></table></div><p><strong>To target other HIV/SIV strains or regions, ACD can design and manufacture <a href="http://acdbio.com/target-probes-made-order">MADE-TO-ORDER Probes</a>  in just 2 weeks. </strong></p></div></div><div class="profile-bottom publication"><div class="classification application-table pub-table"><h2>Related Publications</h2><h3>Recent publications where RNAscope™ assay was used to detect HIV or SIV.</h3><div class="read-more-table"><table><thead><tr><th style="width: 30% !important;">Title</th><th style="width: 30% !important;">Authors</th><th style="width: 16% !important;">Journal</th><th style="width: 16% !important;">PubMed ID</th><th style="width: 9% !important;">Year</th></tr></thead><tbody><tr><td>The meningeal lymphatic system: a route for HIV brain migration?</td><td>Lamers SL, Rose R, Ndhlovu LC, Nolan DJ, Salemi M, Maidji E, Stoddart CA, McGrath MS.</td><td>J Neurovirol. 2015 Nov 16.</td><td>PMID: 26572785</td><td>2015</td></tr><tr><td>CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells.</td><td>Micci L, Alvarez X, Iriele RI, Ortiz AM, Ryan ES, McGary CS, Deleage C, McAtee BB, He T, Apetrei C, Easley K, Pahwa S, Collman RG, Derdeyn CA, Davenport MP, Estes JD, Silvestri G, Lackner AA, Paiardini M.</td><td>PLoS Pathog. 2014 Oct 30;10(10):e1004467.</td><td>PMID: 25356757 | doi: 10.1371/journal.ppat.1004467.</td><td>2014</td></tr><tr><td>B cell follicle sanctuary permits persistent productive simian immunodeficiency virus infection in elite controllers.</td><td>Fukazawa Y, Lum R, Okoye AA, Park H, Matsuda K, Bae JY, Hagen SI, Shoemaker R, Deleage C, Lucero C, Morcock D, Swanson T, Legasse AW, Axthelm MK, Hesselgesser J, Geleziunas R, Hirsch VM, Edlefsen PT, Piatak M Jr, Estes JD, Lifson JD, Picker LJ.</td><td>Nat Med. 2015 Jan 19.</td><td><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=25599132">PMID: 25599132 | doi: 10.1038/nm.3781.</a></td><td>2015</td></tr><tr><td>Effect of Suberoylanilide Hydroxamic Acid (SAHA) Administration on the Residual Virus Pool in a Model of Combination Antiretroviral Therapy-Mediated Suppression in SIVmac239-Infected Indian Rhesus Macaques.</td><td>Del Prete GQ, Shoemaker R, Oswald K, Lara A, Trubey CM, Fast R, Schneider DK, Kiser R, Coalter V, Wiles A, Wiles R, Freemire B, Keele BF, Estes JD, Quiñones OA, Smedley J, Macallister R, Sanchez RI, Wai JS, Tan CM, Alvord WG, Hazuda DJ, Piatak M Jr, Lifson JD.</td><td>Antimicrob Agents Chemother. 2014 Nov;58(11):6790-806.</td><td><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=25182644">PMID: 25182644 |doi: 10.1128/AAC.03746-14.</a></td><td>2014</td></tr><tr><td>Tracking the Luminal Exposure and Lymphatic Drainage Pathways of Intravaginal and Intrarectal Inocula Used in Nonhuman Primate Models of HIV Transmission.</td><td>Smedley J, Turkbey B, Bernardo ML, Del Prete GQ, Estes JD, Griffiths GL, Kobayashi H, Choyke PL, Lifson JD, Keele BF.</td><td>PLoS One. 2014 Mar 25;9(3):e92830.</td><td><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=24667371">PMID: 24667371 | doi: 10.1371/journal.pone.0092830.</a></td><td>2014</td></tr><tr><td>Administration of Panobinostat Is Associated with Increased IL-17A mRNA in the Intestinal Epithelium of HIV-1 Patients</td><td>Christensen AB, Dige A, Vad-Nielsen J, Brinkmann CR, Bendix M, Østergaard L, Tolstrup M, Søgaard OS, Rasmussen TA, Nyengaard JR, Agnholt J, Denton PW.</td><td>Mediators of Inflammation (2015)</td><td>http://dx.doi.org/10.1155/2015/120605</td><td>2015</td></tr></tbody></table></div></div></div></div></div></div></div></div></div> <script 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initESW(null); }; document.body.appendChild(s); } else { initESW('https://service.force.com'); } </script> <script src="//rum-static.pingdom.net/pa-5c133f6e1872b50016000024.js" async></script> <script type="text/javascript">window.NREUM||(NREUM={});NREUM.info={"beacon":"bam.nr-data.net","licenseKey":"NRJS-dd6144c4de227d09eb4","applicationID":"1022125825","transactionName":"YFxbZkpUXBYEVkYNWVkWbEBRGlsLAVBKSkZfSQ==","queueTime":0,"applicationTime":469,"atts":"TBtYEAJOTxg=","errorBeacon":"bam.nr-data.net","agent":""}</script></body> </html>