{"id":138,"date":"2019-02-07T02:24:55","date_gmt":"2019-02-07T02:24:55","guid":{"rendered":"http:\/\/crcmoonshot.org\/?page_id=138"},"modified":"2024-10-28T22:59:23","modified_gmt":"2024-10-28T22:59:23","slug":"pdx-profiling","status":"publish","type":"page","link":"https:\/\/crcmoonshot.org\/?page_id=138","title":{"rendered":"PDX Resources and Profiling"},"content":{"rendered":"<blockquote><p><b><i>400 models with clinical annotation and clinical molecular profile<\/i><\/b><\/p>\n<p><b><i>&gt;125 Annotated PDX Models by WES and RNA seq<\/i><\/b><\/p><\/blockquote>\n<p><a href=\"http:\/\/10.68.3.24:8080\/study\/summary?id=cbiopt_kopetz\" data-wplink-edit=\"true\"><span style=\"color: #993300;\"><strong>cBioPortal database with PDX samples details.\u00a0<\/strong> <\/span><\/a><\/p>\n<p><img loading=\"lazy\" class=\"alignnone size-medium wp-image-240\" src=\"http:\/\/crcmoonshot.org\/wp-content\/uploads\/cbio-300x206.jpg\" alt=\"\" width=\"300\" height=\"206\" srcset=\"https:\/\/crcmoonshot.org\/wp-content\/uploads\/cbio-300x206.jpg 300w, https:\/\/crcmoonshot.org\/wp-content\/uploads\/cbio-768x528.jpg 768w, https:\/\/crcmoonshot.org\/wp-content\/uploads\/cbio.jpg 1021w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/p>\n<p><a href=\"https:\/\/apps.powerapps.com\/play\/e\/Default-2d51fc70-177a-4852-ba7e-54d34883bb15\/a\/f1e4a8f7-c4c3-4cdc-bbb4-bf19b665b42c?source=teamsopenwebsite&amp;screenColor=rgba(184%2C%200%2C%200%2C%201)&amp;hint=5259ee08-6032-4c4a-843d-bfb88cb4b390&amp;tenantId=2d51fc70-177a-4852-ba7e-54d34883bb15\"><span style=\"color: #993300;\"><strong>PDX Model Browser with Clinical Data<\/strong><\/span><\/a><\/p>\n<p>Also, for those inside MDACC, navigate to the <a href=\"https:\/\/teams.microsoft.com\/l\/team\/19%3A83MZAkG10TyDOAt6h1j5LVtbuhMHLUsNUr42tAOX3F81%40thread.tacv2\/conversations?groupId=ace6d690-06da-4ea6-b65c-9e01f6b42b63&amp;tenantId=2d51fc70-177a-4852-ba7e-54d34883bb15\">Kopetz Lab Team<\/a> in Microsoft Teams to explore<\/p>\n<p><a href=\"https:\/\/mdacc.box.com\/s\/lw76eq244kmd6of2al22m6x6vkptzdyl\"><span style=\"color: #993300;\"><strong>RNA Sequencing for PDX samples<\/strong><\/span><\/a><\/p>\n<p>Click the link for access to BOX folder for the RNA, with meta data for the samples, and the gencode V23 transcripts\/genes used for mapping. There are matrices for counts, and TPMS for both transcripts and collapsed to genes.<\/p>\n<p><a href=\"https:\/\/mdacc.box.com\/s\/lw76eq244kmd6of2al22m6x6vkptzdyl\"><span style=\"color: #993300;\"><strong>DNA Sequencing for PDX samples<\/strong><\/span><\/a><\/p>\n<p>Click the link to access to BOX folder for the DNA. This file contains the corresponding .vcf calls from the vendor and the sample ID.<\/p>\n<p>Please contact Scott Kopetz if you require access from external site to the BOX folder.\u00a0 Many thanks to Chris Bristow and Justin Huang for their work on this.<\/p>\n<pre><b><\/b>\n\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>400 models with clinical annotation and clinical molecular profile &gt;125 Annotated PDX Models by WES and RNA seq cBioPortal database with PDX samples details.\u00a0 PDX Model Browser with Clinical Data Also, for those inside MDACC, navigate to the Kopetz Lab Team in Microsoft Teams to explore RNA Sequencing for PDX samples Click the link for &hellip; <a href=\"https:\/\/crcmoonshot.org\/?page_id=138\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">PDX Resources and Profiling<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/pages\/138"}],"collection":[{"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=138"}],"version-history":[{"count":11,"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/pages\/138\/revisions"}],"predecessor-version":[{"id":243,"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=\/wp\/v2\/pages\/138\/revisions\/243"}],"wp:attachment":[{"href":"https:\/\/crcmoonshot.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=138"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}