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epi2melabs-bot committed Dec 19, 2024
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<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[EPI2ME Labs's RSS Feed]]></title><description><![CDATA[Tutorials and workflows for nanopore sequencing.]]></description><link>https://labs.epi2me.io</link><generator>GatsbyJS</generator><lastBuildDate>Wed, 18 Dec 2024 23:49:46 GMT</lastBuildDate><item><title><![CDATA[Modified Base Best Practices and Benchmarking]]></title><description><![CDATA[Explore nanopore modified base best practices and latest model accuracy.]]></description><link>https://labs.epi2me.io/mod-validation-data</link><guid isPermaLink="false">https://labs.epi2me.io/mod-validation-data</guid><pubDate>Tue, 22 Oct 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/18b91467f32be82213c731717219172b/59ccf/pango-buddies.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;Modified bases, including methylation, regulate many biological processes - from eukaryotic gene expression to bacterial immunity.
<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[EPI2ME Labs's RSS Feed]]></title><description><![CDATA[Tutorials and workflows for nanopore sequencing.]]></description><link>https://labs.epi2me.io</link><generator>GatsbyJS</generator><lastBuildDate>Thu, 19 Dec 2024 09:25:55 GMT</lastBuildDate><item><title><![CDATA[Modified Base Best Practices and Benchmarking]]></title><description><![CDATA[Explore nanopore modified base best practices and latest model accuracy.]]></description><link>https://labs.epi2me.io/mod-validation-data</link><guid isPermaLink="false">https://labs.epi2me.io/mod-validation-data</guid><pubDate>Tue, 22 Oct 2024 00:00:00 GMT</pubDate><enclosure url="https://labs.epi2me.io/static/18b91467f32be82213c731717219172b/59ccf/pango-buddies.jpg" length="0" type="image/jpeg"/><content:encoded>&lt;p&gt;Modified bases, including methylation, regulate many biological processes - from eukaryotic gene expression to bacterial immunity.
Methylation plays a pivotal role in human health, influencing cancer development, neurological disorders, cardiovascular diseases, and other conditions through the regulation of cellular processes.&lt;/p&gt;&lt;p&gt;In the context of nanopore sequencing, modified bases can be detected and distinguished through perturbations to the measured ionic current.
These differences are exploited in basecalling, but can also be leveraged in more detailed analyses.&lt;/p&gt;&lt;p&gt;In this post we will outline best practices for performing modified base detection with nanopore sequencing, and present high accuracy benchmark results for three common DNA methylation marks:&lt;/p&gt;&lt;ul&gt;&lt;li&gt;5-methylcytosine (5mC)&lt;/li&gt;&lt;li&gt;5-hydroxymethylcytosine (5hmC)&lt;/li&gt;&lt;li&gt;6-methyladenine (6mA)&lt;/li&gt;&lt;/ul&gt;&lt;p&gt;Benchmarking results are derived from synthetic oligonucleotides, each containing canonical (unmodified) or modified bases within all distinct 5-mer sequence contexts.
We also provide raw data, tools, and step-by-step instructions for running a validation pipeline to replicate these results.&lt;/p&gt;&lt;h2 id=&quot;data-access&quot;&gt;Data Access&lt;/h2&gt;&lt;p&gt;Raw nanopore data for canonical and modified samples, reference sequences, and annotations of canonical and modified positions are available for download.&lt;/p&gt;&lt;p&gt;These datasets allow users to follow the analyses described in this post or expand upon them to conduct more in-depth investigations.
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