{"id":2688,"date":"2020-05-20T10:57:52","date_gmt":"2020-05-20T14:57:52","guid":{"rendered":"https:\/\/www.med.unc.edu\/genomics\/?page_id=2688"},"modified":"2022-02-22T15:06:31","modified_gmt":"2022-02-22T20:06:31","slug":"non-illumina-services","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/genomics\/overview-of-services\/non-illumina-services\/","title":{"rendered":"Alternative Library Services"},"content":{"rendered":"<h2 class=\"section-som\"><span>HTG Sequencing<\/span><\/h2>\n<p style=\"text-align: center;\"><strong>HTSF no longer offers this service. HTSF now collaborate with Dr. Deepak Kumar&#8217;s lab at NCCU. Dr Kumar&#8217;s group makes the different libraries and then sends them to UNC HTSF for sequencing to get the required depth of data. <\/strong><\/p>\n<p style=\"text-align: center;\">Please contact:<\/p>\n<p style=\"text-align: center;\">Lesli Rios-Colon (<a href=\"mailto:lrioscolon@nccu.edu\">lrioscolon@nccu.edu<\/a>)<\/p>\n<p style=\"text-align: center;\">Elana Arthur (<a href=\"mailto:earthur1@nccu.edu\">earthur1@nccu.edu<\/a>)<\/p>\n<h3>HTG Molecular<\/h3>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignleft\" src=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/08\/working_HTG-scaled.jpg\" alt=\"HTG-scaled\" width=\"200\" height=\"2131\" \/>HTG Molecular\u2019s EdgeSeq is a fully automated sample and library preparation platform for targeted RNA sequencing that pairs HTG\u2019s extraction-free, high-specificity Edge Chemistry with the high sensitivity and dynamic range of next-gen sequencing. EdgeSeq enables digital quantitation of miRNA and mRNA expression from difficult sample types such as formalin-fixed, paraffin-embedded (FFPE) tissues, plasma and exosomes.<\/p>\n<p>Assays that are available with HTG include:<\/p>\n<ul>\n<li>HTG EdgeSeq Oncology Biomarker Panel (OBP)<\/li>\n<li>HTG EdgeSeq Precision Immuno-Oncology\u00a0Assay (IO)<\/li>\n<li>HTG EdgeSeq miRNA Whole Transcriptome\u00a0Assay\u00a0(miRNA)<\/li>\n<li>HTG EdgeSeq PATH Panel (PATH)<\/li>\n<li>HTG EdgeSeq Lymphoma Panel (DLBCL)<\/li>\n<li>HTG EdgeSeq Mouse mRNA Tumor Response Panel (TRP)<\/li>\n<\/ul>\n<p>Sequencing and pooling recommendations can be found in the chart below:<\/p>\n<table style=\"width: 100%; border-style: solid; border-color: #007FAE;\" border=\"3\">\n<tbody>\n<tr style=\"height: 23px;\">\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong style=\"color: #007fae;\">Service<\/strong><\/td>\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong style=\"color: #007fae;\">Samples per Pool*<\/strong><\/td>\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong style=\"color: #007fae;\">Platform<\/strong><\/td>\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong style=\"color: #007fae;\">Cycles<\/strong><\/td>\n<\/tr>\n<tr style=\"height: 43px;\">\n<td style=\"width: 25%; height: 43px; text-align: center;\"><strong>HTG (2 million reads per sample)<\/strong><\/td>\n<td style=\"width: 25%; height: 43px; text-align: center;\">8<\/td>\n<td style=\"width: 25%; height: 43px; text-align: center;\">MiSeq<\/td>\n<td style=\"width: 25%; height: 43px; text-align: center;\" rowspan=\"3\">Single End\/50x<\/td>\n<\/tr>\n<tr style=\"height: 23px;\">\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong>HTG (5 million reads per sample)<\/strong><\/td>\n<td style=\"width: 25%; height: 23px; text-align: center;\">48<\/td>\n<td style=\"height: 23px; text-align: center; width: 25%;\">HiSeq 2500<\/td>\n<\/tr>\n<tr style=\"height: 23px;\">\n<td style=\"width: 25%; height: 23px; text-align: center;\"><strong>HTG (2.5 million reads per sample)<\/strong><\/td>\n<td style=\"width: 25%; height: 23px; text-align: center;\">96<\/td>\n<td style=\"text-align: center; width: 25%;\">HS4000<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<div style=\"font-size: 14px;\">*Note: Dependent on the total number of samples that is provided, more efficient pooling plans may be available<\/div>\n<p>&nbsp;<\/p>\n<p>For more information on HTG, please visit <a href=\"https:\/\/www.htgmolecular.com\/\">https:\/\/www.htgmolecular.com\/<\/a><\/p>\n<h2 class=\"section-som\"><span>10X Genomics<\/span><\/h2>\n<em>Please note that 10X whole genome has been discontinued.<\/em><\/p>\n<h3>Single Cell Gene Expression (sc 10X)<\/h3>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright\" src=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/08\/working_10x-scaled.jpg\" alt=\"10x-scaled\" width=\"200\" height=\"1966\" \/>The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells.\u00a0It can help to uncover gene expression variability and identify rare cell types in heterogeneous samples to better characterize cellular contributions during development and disease.<\/p>\n<p><strong>Optionally with Feature Barcoding Technology<\/strong><br \/>\n10X Genomics\u2019s latest improvements allow researchers to:<\/p>\n<ol>\n<li><strong>CRISPR Screening<\/strong>\u00a0&#8211; identify cell-specific CRISPR-mediated perturbations on gene expression via direct capture of gRNAs and polyadenylated mRNAs from the same single cell<\/li>\n<li><strong>Cell Surface Protein<\/strong>\u00a0&#8211;\u00a0measure both gene and cell surface protein expression in the same cell to identify protein isoforms, detect protein for low abundance transcripts, and further increase phenotypic specificity<\/li>\n<\/ol>\n<h3>Single Cell ATAC<\/h3>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignleft\" src=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/08\/RD_Ewa.jpg\" alt=\"Ewa\" width=\"200\" height=\"952\" \/>Single Cell ATAC accelerates the understanding of the regulatory landscape of the genome, thereby providing insights into cell variability. The chromatin profiling of tens of thousands of single cells in parallel allows researchers to see how chromatin compaction and DNA-binding proteins regulate gene expression at high resolution.<\/p>\n<p>Sequencing and pooling recommendations can be found in the table below, A more complete lost of cycles and platforms can be found on <a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-10x_Library_Indexes_And_Sequencing_Requirements_v1_7-2020_FINAL.xlsx\">10x Genomics Library Indexes and Sequencing Requirements<\/a> in Forms and Guides, Alternative Technologies.<\/p>\n<p>Sequencing and pooling recommendations can be found in the table below:<\/p>\n<table style=\"width: 100%; border-style: solid; border-color: #007FAE;\" border=\"3\">\n<tbody>\n<tr>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Service<\/strong><\/td>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Samples per pool<\/strong><\/td>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Platform<\/strong><\/td>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Cycles (Single Cell 3\u2019 V2)<\/strong><\/td>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Cycles (Single Cell 3\u2019 V3)<\/strong><\/td>\n<td style=\"text-align: center;\"><strong style=\"color: #007fae;\">Cycles (ATAC seq)<\/strong><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;\" rowspan=\"5\">\n<ul>\n<li>10x 3&#8242; trans<\/li>\n<li>ATACseq 5000 cells<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/td>\n<td style=\"text-align: center;\">1<\/td>\n<td style=\"text-align: center;\">HiSeq 4000<\/td>\n<td style=\"text-align: center;\" rowspan=\"5\">26x8x98<\/td>\n<td style=\"text-align: center;\" rowspan=\"5\">28x8x91<\/td>\n<td style=\"text-align: center;\" rowspan=\"5\">50x8x16x50<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;\">3<\/td>\n<td style=\"text-align: center;\">NovaSeq SP<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;\">6<\/td>\n<td style=\"text-align: center;\">NovaSeq S1<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;\">15<\/td>\n<td style=\"text-align: center;\">NovaSeq S2<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: center;\">40<\/td>\n<td style=\"text-align: center;\">NovaSeq S4<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<div style=\"font-size: 14px;\">*Note: 5000 living cells are required for successful library preparation. Please provide more cells to compensate for any cell death that may occur during transportation to HTSF. For 5000 cells, the HTSF recommends providing 8000 cell input.<br \/>\n** Note: For each set of 5000 living cells, sequencing should yield approximately 250 million clusters<\/div>\n<div><\/div>\n<p style=\"text-align: center;\"><strong>HTSF is unable to offer 10X Genomics library prep at this time. Please contact the Advanced Analytics Core (AACORE). There is detailed AACORE info and contact listed on this website under the About Us section, <a href=\"https:\/\/www.med.unc.edu\/genomics\/about\/unc-htsf-collaborating-core\/\">UNC HTSF Collaborating Cores page<\/a>. AACORE offers complete single cell services for 10 Genomics library prep. When deeper sequencing is required, AACORE transfers the 10x pools to the HTSF for sequencing.<\/strong><\/p>\n<p style=\"text-align: left;\">For more information on 10X genomics, please visit <a href=\"https:\/\/www.10xgenomics.com\/ \">https:\/\/www.10xgenomics.com\/<\/a><\/p>\n<h2 class=\"section-som\"><span>Relevant Alternative Services Forms and Guides <\/span><\/h2>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-DNA-and-RNA-Sample-Preparation-Requirement-Guide_V6_12-2021_FINAL-1.pdf\">HTSF Sample Preparation Requirement Guide <\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-Illumina_Sequencing_Platform_Comparison_Chart_v7_12-2021_FINAL.pdf\">Illumina Platform Comparison and Specification Table<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-NovaSeq-Requirements-and-Pooling-Suggestions_v3_7-2020_FINAL.pdf\">NovaSeq Requirements<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-Approved-Container-Requirements_v5_7-2020_FINAL.pdf\">Approved Containers Information <\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-10x_Manifest_HTSF_Made_Libraries_v1_7-2020_FINAL.xlsx\">10x Genomics Submission Manifest for HTSF Made Libraries<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-10x_Library_Indexes_And_Sequencing_Requirements_v1_7-2020_FINAL.xlsx\">10x Genomics Library Indexes and Sequencing Requirements<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-10x_Manifest_With_-Indexes_and_Seq_Requirements_For_Study_Made_Libraries_v9_7-2020_FINAL-1.xlsx\">10x Genomics Manifest for Study Made Libraries with Indexes and Sequencing Requirements<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-Novaseq-Whitepaper_v45_7-2020_FINAL.pdf\">NovaSeq White Paper<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-HTG_WhitePaper_V2_7-2020_FINAL.pdf\">HTG White Paper<\/a><br \/>\n<a href=\"https:\/\/www.med.unc.edu\/genomics\/wp-content\/uploads\/sites\/708\/2020\/07\/HTSF-10x_Genomics_WhitePaper_V2_7-2020_FINAL.pdf\">10x Genomics White Paper<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>HTSF no longer offers this service. HTSF now collaborate with Dr. Deepak Kumar&#8217;s lab at NCCU. Dr Kumar&#8217;s group makes the different libraries and then sends them to UNC HTSF for sequencing to get the required depth of data. Please contact: Lesli Rios-Colon (lrioscolon@nccu.edu) Elana Arthur (earthur1@nccu.edu) HTG Molecular HTG Molecular\u2019s EdgeSeq is a fully &hellip; <a href=\"https:\/\/www.med.unc.edu\/genomics\/overview-of-services\/non-illumina-services\/\" aria-label=\"Read more about Alternative Library Services\">Read more<\/a><\/p>\n","protected":false},"author":64010,"featured_media":0,"parent":2650,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2688","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages\/2688","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/users\/64010"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/comments?post=2688"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages\/2688\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages\/2650"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/media?parent=2688"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}