{"id":380,"date":"2024-09-16T11:30:49","date_gmt":"2024-09-16T18:30:49","guid":{"rendered":"https:\/\/blogs.oregonstate.edu\/cqls\/?p=380"},"modified":"2024-11-21T08:44:03","modified_gmt":"2024-11-21T16:44:03","slug":"bluepippin-dna-size-selection","status":"publish","type":"post","link":"https:\/\/blogs.oregonstate.edu\/cqls\/2024\/09\/16\/bluepippin-dna-size-selection\/","title":{"rendered":"BluePippin DNA Size Selection"},"content":{"rendered":"\n<p><em>Elizabeth Zepeda and Katie Carter<\/em><\/p>\n\n\n\n<p>Our BluePippin instrument is used for DNA size selection. Several genomic applications benefit from collecting only DNA fragments within a specified size range from a pool of DNA. This service is often used before Illumina sequencing to remove undesired PCR peaks or before long read sequencing to increase the proportion of fragments greater than a given length in a library.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"511\" height=\"361\" src=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-6.png\" alt=\"\" class=\"wp-image-381\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-6.png 511w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-6-300x212.png 300w\" sizes=\"auto, (max-width: 511px) 100vw, 511px\" \/><\/figure>\n\n\n\n<p>Using pulsed-field electrophoresis on pre-cast gel cassettes, a DNA sample is separated and fragments within the target range are eluted into buffer. Each cassette can run up to 5 samples at once. Up to 5 ug of DNA can be loaded into each well.<\/p>\n\n\n\n<p>The following cassettes are available at CQLS:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>3% agarose, 100-250bp<\/li>\n\n\n\n<li>2% agarose, 100-600bp<\/li>\n\n\n\n<li>1.5% agarose, 250bp \u2013 1.5kb<\/li>\n\n\n\n<li>0.75% agarose, 1-50kb<\/li>\n<\/ul>\n\n\n\n<p>The desired size range must lie within the total size range capability of the cassette. For example, between 200-350 bp on a 2% agarose cassette would be an acceptable range.<\/p>\n\n\n\n<p>The expected collection yield of target sizes is approximately 50-80% based on product validation studies. Yield can vary greatly depending on the desired range and input fragment sizes.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"928\" height=\"838\" src=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-7.png\" alt=\"\" class=\"wp-image-384\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-7.png 928w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-7-300x271.png 300w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/3381\/files\/2024\/09\/image-7-768x694.png 768w\" sizes=\"auto, (max-width: 928px) 100vw, 928px\" \/><figcaption class=\"wp-element-caption\">Before and after size selection of Illumina sequencing library to remove undesired peak at approx. 300 bp<\/figcaption><\/figure>\n\n\n\n<p>Contact Katie Carter for inquiries about this service.<\/p>\n\n\n\n<p>Source: <a href=\"http:\/\/sagescience.com\">sagescience.com<\/a><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Elizabeth Zepeda and Katie Carter Our BluePippin instrument is used for DNA size selection. Several genomic applications benefit from collecting only DNA fragments within a specified size range from a pool of DNA. This service is often used before Illumina sequencing to remove undesired PCR peaks or before long read sequencing to increase the proportion&hellip; <a href=\"https:\/\/blogs.oregonstate.edu\/cqls\/2024\/09\/16\/bluepippin-dna-size-selection\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":14192,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[97201],"tags":[],"class_list":["post-380","post","type-post","status-publish","format-standard","hentry","category-laboratory"],"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/posts\/380","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/users\/14192"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/comments?post=380"}],"version-history":[{"count":3,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/posts\/380\/revisions"}],"predecessor-version":[{"id":385,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/posts\/380\/revisions\/385"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/media?parent=380"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/categories?post=380"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/cqls\/wp-json\/wp\/v2\/tags?post=380"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}