{"id":2957,"date":"2020-06-03T11:54:44","date_gmt":"2020-06-03T15:54:44","guid":{"rendered":"https:\/\/www.med.unc.edu\/genomics\/?page_id=2957"},"modified":"2022-02-22T15:18:51","modified_gmt":"2022-02-22T20:18:51","slug":"qaqc-clean-up-methods","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/genomics\/qaqc\/qaqc-clean-up-methods\/","title":{"rendered":"QAQC Clean Up Methods"},"content":{"rendered":"

My QAQC results show one of these failures\u2026what do I do?<\/em><\/h4>\n

HTSF will discuss with you the best way to resolve an issue after we run QAQC.<\/p>\n

RNA Clean Up Methods<\/span><\/h2>\n\n\n\n\n\n\n\n
Clean Up Method<\/strong><\/td>\nResolution for the following Issues<\/strong><\/td>\n<\/tr>\n
EtOH cleanup<\/strong><\/td>\ndegraded samples<\/u><\/strong><\/td>\n<\/tr>\n
RNA XP bead cleanup<\/strong><\/td>\ngood for transferring samples<\/u><\/strong> if not supplied in DNase\/RNase-Free H2O OR potential contamination<\/u><\/strong> of the sample<\/td>\n<\/tr>\n
RNA Clean and Concentrator (Zymo research)<\/strong><\/td>\nColumn cleanup;<\/u><\/strong> use to DNase treat RNA samples<\/td>\n<\/tr>\n
Pippin Prep Size Selection (gel size selection)<\/strong><\/td>\nbest for high resolution bp selection<\/u><\/strong>; preferred for small RNA cleanup<\/u><\/strong> which has primer dimers at 140-160 bp and a library peak at ~180 bp<\/p>\n

 <\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

DNA Clean Up Methods<\/span><\/h2>\n\n\n\n\n\n\n\n\n
Clean Up Method<\/strong><\/td>\nResolution for the following Issues<\/strong><\/td>\n<\/tr>\n
2x Beadwash<\/strong><\/td>\ngood for maximum recovery<\/u><\/strong> of sample and to transfer samples<\/u><\/strong> from improper submission solution (ex: PCR buffer)<\/p>\n

*good for any type of dsDNA material*<\/em><\/td>\n<\/tr>\n

0.8x Beadwash<\/strong><\/td>\n <\/p>\n

aggressive beadwash to remove primer dimers in the 100-160 bp range<\/u><\/strong> when library size is over 300 bp<\/td>\n<\/tr>\n

1.0x Beadwash<\/strong><\/td>\n <\/p>\n

less aggressive beadwash to remove primer dimers in the 100-160 bp range<\/u><\/strong> when library size is ~250 bp<\/p>\n

 <\/td>\n<\/tr>\n

SPRI (two-sided beadwash)<\/strong><\/td>\n <\/p>\n

good for general size selection between 160 bp and 600 bp<\/u><\/strong><\/p>\n

 <\/td>\n<\/tr>\n

Pippin Prep Size Selection (gel size selection)<\/strong><\/td>\n <\/p>\n

best for high resolution bp selection<\/u><\/strong>; preferred for small RNA cleanup which has primer dimers at 140-160 bp and a library peak at ~180 bp<\/p>\n

 <\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

My QAQC results show one of these failures\u2026what do I do? HTSF will discuss with you the best way to resolve an issue after we run QAQC. Clean Up Method Resolution for the following Issues EtOH cleanup degraded samples RNA XP bead cleanup good for transferring samples if not supplied in DNase\/RNase-Free H2O OR potential … Read more<\/a><\/p>\n","protected":false},"author":64010,"featured_media":0,"parent":2936,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2957","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\/2957","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=2957"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages\/2957\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/pages\/2936"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/genomics\/wp-json\/wp\/v2\/media?parent=2957"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}