{"search_session":{},"preferences":{"l":"es","queryLanguage":"es"},"patentId":"US_9097708_B2","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"134-171-269-535-24X","entityRefType":"PATENT"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":8906,"type":"PATENT","title":"Univ Pennsylvania Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":24238,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8221,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
Search applicants and owners= \"Univ Pennsylvania\", \"Pennsylvania Univ\", \"Univ Penns*\", \"Penn* Univ\", \"University of Pennsylvania\", \"Pennsylvania University\".
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Search applicants and owners= \"Univ Pennsylvania\", \"Pennsylvania Univ\", \"Univ Penns*\", \"Penn* Univ\", \"University of Pennsylvania\", \"Pennsylvania University\".
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(a) preparing an RNase footprinting library, wherein said preparation comprises:\n\ni. exposing a eukaryotic cell to a crosslinking agent;\nii. obtaining a nucleic acid-containing sample from the cell;\niii. treating a first fraction of the sample with a single-stranded RNase;\niv. thereafter treating the first fraction with a protease or proteinase;\nv. treating a second fraction of the sample with a double-stranded RNase;\nvi. thereafter treating the second fraction with a protease or proteinase;\nvii. isolating RNA from the first fraction and the second fraction; and\nviii. preparing a strand specific sequence library from the isolated RNA;\n
(b) preparing an RNase control library, wherein said preparation comprises:\n\ni. exposing a eukaryotic cell to a crosslinking agent;\nii. obtaining a nucleic acid-containing sample from the cell;\niii. treating a first fraction of the sample with protease or proteinase;\niv. thereafter treating the first fraction of the sample with a single-stranded RNase;\nv. treating a second fraction of the sample with protease or proteinase;\nvi. thereafter treating the second fraction of the sample with a double-stranded RNase;\nvii. isolating RNA from the first fraction and the second fraction; and\nviii. preparing a strand specific sequence library from the isolated RNA,\n
(c) identifying candidate protein binding sites within the RNase footprinting library; and\n
(d) identifying sequence level motifs within the candidate protein binding sites."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the sample is obtained by lysing the cell."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 2, further comprising treating the sample with a DNase following cell lysis."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying candidate protein binding sites comprises identifying protein protected sites; and comparing the protein protected sites with previously published protein data."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein identifying sequence level motifs comprises selecting a site specific candidate protein binding site from the candidate protein binding sites; and using a motif finding algorithm to identify at least one motif from the site specific candidate protein binding site."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 5, wherein the site specific candidate binding site is found in the 5′ UTR, the protein coding region, or the 3′ UTR."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 5, further comprising validating the motif by performing a competitive pull-down assay."],"number":7,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}