{"id":"W4379467257","doi":"10.21769/bioprotoc.4688","title":"Revised iCLIP-seq Protocol for Profiling RNA–protein Interaction Sites at Individual Nucleotide Resolution in Living Cells","year":2023,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"RNA Research and Splicing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Canadian Institutes of Health Research","keywords":"Polyadenylation; Computational biology; RNA; RNA-binding protein; Biology; Binding site; Immunoprecipitation; Riboswitch; Genetics; Gene; Non-coding RNA","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001164694,0.0002479299,0.0002128781,0.0002194816,0.0002336172,0.0001096949,0.000304594,0.0002277901,0.00006728533],"category_scores_gemma":[0.0005458342,0.000232329,0.0001417402,0.0003514669,0.00005947348,0.00002507268,0.0003837225,0.0002020659,0.00008285646],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001232228,"about_ca_system_score_gemma":0.0001255584,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003864251,"about_ca_topic_score_gemma":0.0001207393,"domain_scores_codex":[0.9977115,0.0002028282,0.000510819,0.0006198033,0.0003054417,0.0006495748],"domain_scores_gemma":[0.9990678,0.00006373499,0.0002138637,0.0004001745,0.0001220079,0.0001323568],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001112111,0.00009435332,0.003212056,0.0006424306,0.00001598551,0.000005589553,0.00003501852,0.00008354735,0.9879059,0.00001768861,0.004811469,0.002063864],"study_design_scores_gemma":[0.002593378,0.0007041733,0.002482653,0.0004762098,0.000003699167,0.000002337811,0.00009514316,0.002959641,0.9343737,0.00003332654,0.05597319,0.0003025359],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"protocol","genre_gemma":"protocol","genre_scores_codex":[0.2001232,5.961046e-7,0.0001437794,0.00007117941,0.00002101237,0.799327,0.00002129562,0.00005951976,0.0002324242],"genre_scores_gemma":[0.008704659,3.016882e-7,0.001838804,0.00005275423,0.0003190496,0.9866089,0.0000822287,0.00005360064,0.002339692],"genre_candidate":"protocol","genre_consensus":"protocol","teacher_disagreement_score":0.1914185,"threshold_uncertainty_score":0.9474102,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05757904599849727,"score_gpt":0.3755177266782632,"score_spread":0.3179386806797659,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}