{"id":467,"date":"2024-04-25T20:22:01","date_gmt":"2024-04-25T20:22:01","guid":{"rendered":"https:\/\/winterdev.cc\/nwgc-dev\/?page_id=467"},"modified":"2024-04-25T20:22:01","modified_gmt":"2024-04-25T20:22:01","slug":"getting-started","status":"publish","type":"page","link":"https:\/\/nwgc.gs.washington.edu\/wordpress\/services\/already-prepped-libraries\/getting-started\/","title":{"rendered":"Getting Started"},"content":{"rendered":"<p>Thank you for your interest in the NWGC!<\/p>\n<p>Below is the step-by-step process for getting your already constructed libraries sequenced. Please review these steps carefully and if you have any questions, please don&#8217;t hesitate to ask.<\/p>\n<h3 class=\"wp-block-heading\">1.) Request a Quote<\/h3>\n<p>To request a quote, please email&nbsp;<a href=\"mailto:nwgc@uw.edu\">nwgc@uw.edu<\/a>&nbsp;with the following information:<\/p>\n<p>Investigator Name<br \/>Phone Number<br \/>Email Address<br \/>Request Information<\/p>\n<p>*Request Information should include as much detail as possible about your project requirements. For guidance, please see the Getting Started pages under your project type for more information.<\/p>\n<p>The NWGC will send you a quote based on your project specifications. Do not send any samples before reviewing the quote and returning the signed quote or purchase order to the NWGC.<\/p>\n<h3 class=\"wp-block-heading\">2.) Sample Submission Information<\/h3>\n<p>Once a quote is received and signed, please email the NWGC Sequencing Team at <a href=\"mailto:nwgcseq@uw.edu\">nwgcseq@uw.edu<\/a> to receive the Sample Submission Form.  Please fully fill out the form and return it to&nbsp;<a href=\"mailto:nwgcseq@uw.edu\">nwgcseq@uw.edu<\/a> prior to sample drop-off or delivery.  Please also send all the barcode information for your library(s).<\/p>\n<p>**We use the information provided to load the sequencing instruments and generate FASTQs. Please make sure it is as accurate as possible.<\/p>\n<p>Please follow the guidelines for submission below:<\/p>\n<h3 class=\"wp-block-heading\">Required Sample Information:<\/h3>\n<ul class=\"wp-block-list\">\n<li>Please only submit samples in 1.5mL \u2013 2.0mL tubes with snap-caps or screw caps!<\/li>\n<li>Please avoid naming samples 1, 2, 3 etc. and include a unique identifier in order for us to keep better track of your sample.<\/li>\n<li>The molarity of your final submission, whether that be individual libraries or a pool. Please use something more accurate than a Nanodrop, like qPCR for example.<\/li>\n<\/ul>\n<p><em>Short-Read Specific: <\/em><\/p>\n<ul class=\"wp-block-list\">\n<li>The read length for your sequencing run. (PE25 = 50 cycles, SE50 = 50 cycles).<\/li>\n<li>The number of base pairs in your index sequence. (ie. +8,+8+8,+10,+10+10)<\/li>\n<li>The actual index sequences, listed in the forward orientation, and what samples they correspond to. We use this to demultiplex your libraries. Please list on a new page or attach a separate file.<\/li>\n<li>The required primer type. If using custom primers (non-Illumina), please provide them at 100uM.<\/li>\n<li>The type of molecule (RNA, genome) or specialized prep (ChIP-seq, ATAC-seq) we will be sequencing.<\/li>\n<\/ul>\n<p><em>Long-Read Specific:<\/em><\/p>\n<ul class=\"wp-block-list\">\n<li>The movie length needed. (12, 24, 30 hours)<\/li>\n<li>Number of SMRTcells and coverage needed per sample or library pool.<\/li>\n<li>Barcode kit type and specific barcodes per sample.<\/li>\n<li>Type of library prep\/ kit type used.<\/li>\n<li>If any additional analysis is needed via SMRTlink.<\/li>\n<\/ul>\n<h3 class=\"wp-block-heading\">4.) QC Results<\/h3>\n<p>All short-read sequencing samples will be run on the Bioanalyzer and Qubit.  All long-read sequencing samples will be run on the Femto and Qubit.  QC results will be emailed to the investigator before sequencing.<\/p>\n<h3 class=\"wp-block-heading\">5.) Data Delivery\/Globus Access<\/h3>\n<p>Globus is a service provider that manages login credentials and coordinates transfers between organizations. Please visit the<em>\u00a0Data Delivery<\/em>\u00a0section for more information.<\/p>\n<p>Once your run is complete, we will send you an email with a link to your specific Globus folder where the run file is located.<\/p>\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-wide\"\/>\n<h2 class=\"wp-block-heading\">Supplemental Info:<\/h2>\n<ul class=\"wp-block-list\">\n<li>Below are the minimum volume requirements, based on our minimum molarity accepted per sequencing platform:<\/li>\n<\/ul>\n<figure class=\"wp-block-table\">\n<table>\n<tbody>\n<tr>\n<td><strong>Sequencing Platform<\/strong><\/td>\n<td><strong>Minimum Molarity<\/strong><\/td>\n<td><strong>Minimum Volume<\/strong><\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq S4<\/td>\n<td>5nM<\/td>\n<td>130uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq S2<\/td>\n<td>5nM<\/td>\n<td>55uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq SP\/S1<\/td>\n<td>5nM<\/td>\n<td>35uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq X Plus 1.5B<\/td>\n<td>5nM<\/td>\n<td>20uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq X Plus 10B<\/td>\n<td>5nM<\/td>\n<td>60uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NovaSeq X Plus 25B<\/td>\n<td>5nM<\/td>\n<td>100uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae NextSeq 500 MO or HO<\/td>\n<td>5nM<\/td>\n<td>10uL<\/td>\n<\/tr>\n<tr>\n<td>Illumina\u00ae MiSeq<\/td>\n<td>4nM<\/td>\n<td>20uL<\/td>\n<\/tr>\n<tr>\n<td>Element AVITI\u2122 Cloudbreak Freestyle<\/td>\n<td>5nM<\/td>\n<td>20uL<\/td>\n<\/tr>\n<\/tbody>\n<\/table><figcaption class=\"wp-element-caption\"><strong>*Volume required will be less if the nM is great than 5nM. **Volume needed for QC is included.<\/strong><\/figcaption><\/figure>\n<figure class=\"wp-block-table\">\n<table>\n<tbody>\n<tr>\n<td><strong>Long-Read Sequencing Platform<\/strong><\/td>\n<td><strong>Minimum Concentration<\/strong><\/td>\n<td><strong>Minimum order<\/strong><\/td>\n<\/tr>\n<tr>\n<td>PacBio Revio\u2122<\/td>\n<td>20-60ng\/ul in 28ul (concentration varies based on insert size)<\/td>\n<td>SMRT\u2122 Cell<\/td>\n<\/tr>\n<tr>\n<td>Oxford Nanopore Technologies\u00ae<\/td>\n<td>&nbsp;2-10ug (concentration varies based on prep type and coverage needed)<\/td>\n<td>Flow cell<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/figure>\n<ul class=\"wp-block-list\">\n<li>QC is included in the pricing and will be run in-house using Qubit and Bioanalyzer\/Femto for every submission. If you have any Bioanalyzer traces, please include with your sample submission.<\/li>\n<li>Our QC data will be used to verify the molarity of your submission. The Bioanalyzer\/Femto also examines possible adapter peaks, mean insert size, and overall sample quality. The Qubit gives concentration (ng\/uL) and is taken in tandem with the BA insert size to yield molarity (nM). (ng\/uL)*(1,000,000) \/ (insert size)*(660) = nM<\/li>\n<li>Please include your sample barcode list with sample submission form prior to the sample run. <\/li>\n<li>For short-read sequencing, FASTQ is the standard data delivery type. If you require an alternative, please inquire before submitting as an additional charge may occur.<\/li>\n<li>Once emailed that your data is ready on Globus, you will have 120 days to access it before it is deleted indefinitely.<\/li>\n<li>For 10X Genomics Sequencing we offer two pipelines: CellRanger version 7.0.1 and CellRanger-ATAC version 1.2.0.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Thank you for your interest in the NWGC! Below is the step-by-step process for getting your already constructed libraries sequenced. Please review these steps carefully and if you have any questions, please don&#8217;t hesitate to ask. 1.) Request a Quote To request a quote, please email&nbsp;nwgc@uw.edu&nbsp;with the following information: Investigator NamePhone NumberEmail AddressRequest Information *Request Information should include as much detail as possible about your project requirements. For guidance, please see the Getting Started pages under your project type for&#8230;<\/p>\n<div><a class=\"more-link\" href=\"https:\/\/nwgc.gs.washington.edu\/wordpress\/services\/already-prepped-libraries\/getting-started\/\">Continue reading <span class=\"screen-reader-text\">Getting Started<\/span><\/a><\/div>\n","protected":false},"author":2,"featured_media":0,"parent":306,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-467","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/467","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/comments?post=467"}],"version-history":[{"count":0,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/467\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/pages\/306"}],"wp:attachment":[{"href":"https:\/\/nwgc.gs.washington.edu\/wordpress\/wp-json\/wp\/v2\/media?parent=467"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}