{"id":120,"date":"2012-08-16T16:30:00","date_gmt":"2012-08-16T20:30:00","guid":{"rendered":"https:\/\/med.sites.unc.edu\/vironomics\/sequencing-1\/copy_of_454-gs-junior-next-generation-sequencing\/"},"modified":"2018-07-12T09:46:07","modified_gmt":"2018-07-12T13:46:07","slug":"copy_of_454-gs-junior-next-generation-sequencing","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/vironomics\/sequencing-1\/copy_of_454-gs-junior-next-generation-sequencing\/","title":{"rendered":"Vironomics Core Next Generation Sequencing"},"content":{"rendered":"<p><!-- portlet_header --><\/p>\n<p><!-- portlet_above --><\/p>\n<p><!-- description --><\/p>\n<h2><b>Overview<\/b><\/h2>\n<p class=\" \"><span style=\"color: #000000\"><span style=\"color: #000000\">We can sequence a wide variety of organisms, we are not limited to viruses.<\/span> The sequencers in the core are ideal for longer DNA fragment sequencing. The Ion Torrent PGM is capable of 200-400bp read lengths. The Ion Torrent S5 has the ability to increase that to 600bp<b>\u00aa<\/b> and increases the number of reads\/depth available. Many clients use the longer reads for large genomes, <em>de novo<\/em> sequencing, 16S sequencing, long amplicons, etc. <\/span><\/p>\n<p class=\" \"><span style=\"color: #000000\">Submission for one platform or the other generally depends on a) fragment length b) amount of double-stranded DNA available for sequencing and\/or c) number of reads needed for your experiment.<\/span><\/p>\n<p class=\" \"><span style=\"color: #000000\"><b>\u00aa<\/b> 600bp costs more, please add an extra emPCR rate to the cost of the run<br \/>\n<\/span><\/p>\n<h3><span style=\"color: #000000\"><strong>Examples of our seq runs and quality scores, <a class=\"internal-link\" title=\"\" href=\"https:\/\/www.med.unc.edu\/vironomics\/sequencing-1\/our-best-ion-runs\" target=\"_blank\" rel=\"noopener noreferrer\">click here<\/a><\/strong><\/span><\/h3>\n<h2><span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">SEQUENCING OPTIONS<\/span><\/strong><\/span><\/h2>\n<ol>\n<li><span style=\"color: #000000\"><strong><em>Your custom project for Ion Torrent<\/em><\/strong><\/span>\n<ul>\n<li><span style=\"color: #000000\">Please discuss with core manager details and costs<\/span><\/li>\n<\/ul>\n<\/li>\n<li><strong><span class=\"description\"><a class=\"internal-link\" title=\"\" href=\"https:\/\/www.med.unc.edu\/vironomics\/sequencing-1\/str-cell-line-authentication\" target=\"_blank\" rel=\"noopener noreferrer\">Next Generation Sequencing: Cell Line verification<\/a><\/span><\/strong>\n<ul>\n<li><b>NIH Grant Applications authentication of key biological and\/or chemical resources<\/b><\/li>\n<li><span class=\"description\"><span class=\"description\">Utilizing our <strong>Ion Torrent<\/strong> sequencers (more reads) allows most runs to accommodate a greater number of samples. This commercially available option, <a class=\"external-link\" title=\"\" href=\"https:\/\/www.thermofisher.com\/content\/dam\/LifeTech\/global\/tactic-assets\/Q4-2015\/forensics\/PG1596-PJT1557-COL31170-HID-Ion-Precision-ID-System-Broch-Global-FHR.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">Precision ID NGS<\/a> STR, allows for a plug-n-play analysis, which decreases the need for specialized bioinformatics. For more detailed information, please go to the <a class=\"internal-link\" title=\"\" href=\"https:\/\/www.med.unc.edu\/vironomics\/sequencing-1\/str-cell-line-authentication\" target=\"_blank\" rel=\"noopener noreferrer\">dedicated page here<\/a>.<\/span><\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"color: #000000\"><strong>Plasmid Verification: <\/strong><span class=\"description\">We have had success with plasmid verification for various clients<\/span><\/span><\/li>\n<li><span style=\"color: #000000\"><strong>Whole Genome de novo sequencing: <\/strong>See our publications lists for examples<\/span><\/li>\n<li><strong>Targeted Amplicon sequencing<\/strong>: custom or see off-the-shelf <a class=\"external-link\" title=\"\" href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/next-generation-sequencing\/ion-torrent-next-generation-sequencing-workflow\/ion-torrent-next-generation-sequencing-select-targets\/ampliseq-target-selection.html\" target=\"_blank\" rel=\"noopener noreferrer\">Ion panels<\/a><\/li>\n<li><strong>Exome sequencing<\/strong><\/li>\n<li><strong>RNAseq (strandedness retained)<\/strong><\/li>\n<\/ol>\n<h2><strong><span style=\"text-decoration: underline;color: #000000\">Ion Torrent PGM and S5 SUBMISSION REQUIREMENTS<\/span><br \/>\n<\/strong><\/h2>\n<p class=\" \">They have a 97.5% per base <em>accuracy up to 5 homopolymers<\/em>.<\/p>\n<p>\u226510\u226520<\/p>\n<table class=\"table table-striped\" border=\"1\">\n<tbody>\n<tr>\n<th><span style=\"text-decoration: underline\"><strong>Submission requirements<\/strong><\/span><\/th>\n<th><span style=\"text-decoration: underline\"><strong>DNA Needs Fragmentation<\/strong><\/span><br \/>\n<strong>(gDNA, BAC, Plasmid, etc.)<\/strong><\/th>\n<th><span style=\"text-decoration: underline\"><strong>DNA Already Fragmented<\/strong><\/span><strong><br \/>\n(amplicons\u00a4,<br \/>\ndouble stranded cDNA, etc.)<\/strong><\/th>\n<th><strong><span style=\"text-decoration: underline\">Total RNA\u2020<\/span><\/strong><\/th>\n<th><strong><span style=\"text-decoration: underline\">Poly(A) RNA<\/span><\/strong>\u2020<\/th>\n<th><span style=\"text-decoration: underline\"><strong>rRNA depleted RNA<\/strong><\/span>\u2020<\/th>\n<\/tr>\n<tr>\n<td><strong><em>Purity<\/em><\/strong><\/td>\n<td>260\/280 ratio \u2265 1.8<\/td>\n<td>260\/280 ratio \u2265 1.8<\/td>\n<td>RIN \u2265 7<\/td>\n<td>n\/a<\/td>\n<td>n\/a<\/td>\n<\/tr>\n<tr>\n<td><strong><em>length<\/em><\/strong><\/td>\n<td>\u2265 1000bp<\/td>\n<td>260-410bp<\/td>\n<td>n\/a<\/td>\n<td>n\/a<\/td>\n<td>n\/a<\/td>\n<\/tr>\n<tr>\n<td><strong><em>minimum ng\/uL*<\/em><\/strong><\/td>\n<td>\u2265 1.4<\/td>\n<td>\u2265 0.2<\/td>\n<td>\u22651.9<\/td>\n<td>\u2265 0.2<\/td>\n<td>\u2265 1.3<\/td>\n<\/tr>\n<tr>\n<td><strong><em>minimum total ng<\/em><\/strong><\/td>\n<td>50<\/td>\n<td>10<\/td>\n<td>100<\/td>\n<td>1<\/td>\n<td>10<\/td>\n<\/tr>\n<tr>\n<td><strong><em>ave volume to send (dependent<br \/>\non concentration)<\/em><\/strong><\/td>\n<td>40-55<\/td>\n<td>10-30<\/td>\n<td><\/td>\n<td>\u2265 10<\/td>\n<td>\u2265 20<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u00a4 <span style=\"line-height: 1.43em\">Amplicons<\/span><span style=\"line-height: 1.43em\">: This technology is sensitive to primer-dimers, please contact Core Manager for protocol of removing small fragments using AMPure beads. Also, if multiplexing samples, each amplicon should be similar in length.<\/span><\/p>\n<p>* <span style=\"line-height: 1.43em\">NanoDrop is not accurate<\/span><span style=\"line-height: 1.43em\"> for assessing sequencing samples. If you do need to use the NanoDrop, please send <\/span><span style=\"line-height: 1.43em\">double the required input.<\/span><\/p>\n<p>\u2020 Please ensure your samples do not have contaminating genomic DNA by performing a RT-minus reaction for each of your samples.<\/p>\n<h2><span style=\"text-decoration: underline\"><span style=\"color: #000000\"><strong><span style=\"line-height: 1.3em\">Ordering<\/span><\/strong><\/span><\/span><\/h2>\n<p><a class=\"internal-link\" title=\"\" href=\"https:\/\/www.med.unc.edu\/vironomics\/services\/sample-submission\" target=\"_blank\" rel=\"noopener noreferrer\"><span style=\"text-decoration: underline\">Submission requirements here<\/span><\/a>.<\/p>\n<p><a href=\"https:\/\/www.med.unc.edu\/vironomics\/about-us-2\/staff2\/\">Vironomics Core Manager<\/a>: 919-843-5292<\/p>\n<div class=\"alert alert-gray\"><strong>Illumina Platforms<\/strong><\/div>\n<p class=\" \">On a custom basis we can make Illumina libraries and assist with submitting them to another facility. This generally requires purchase of an entire library kit since we do not keep these in stock. Please contact the Core manager to inquire about cost and staff availability.<\/p>\n<p class=\" \">If you have only a few samples please consider having the facility with the sequencing instrument make your libraries. Please see <a class=\"external-link\" title=\"\" href=\"http:\/\/www.med.unc.edu\/corefacilities\" target=\"_blank\" rel=\"noopener noreferrer\">UNC Research Core Facilities<\/a> page to explore other facilities.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview We can sequence a wide variety of organisms, we are not limited to viruses. The sequencers in the core are ideal for longer DNA fragment sequencing. The Ion Torrent PGM is capable of 200-400bp read lengths. The Ion Torrent S5 has the ability to increase that to 600bp\u00aa and increases the number of reads\/depth &hellip; <a href=\"https:\/\/www.med.unc.edu\/vironomics\/sequencing-1\/copy_of_454-gs-junior-next-generation-sequencing\/\" aria-label=\"Read more about Vironomics Core Next Generation Sequencing\">Read more<\/a><\/p>\n","protected":false},"author":33839,"featured_media":0,"parent":37,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-120","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/pages\/120","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/users\/33839"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/comments?post=120"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/pages\/120\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/pages\/37"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/vironomics\/wp-json\/wp\/v2\/media?parent=120"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}