{"id":"W1994941758","doi":"10.1038/nprot.2013.088","title":"Chromatin tandem affinity purification sequencing","year":2013,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Ottawa; Ottawa Hospital","funders":"National Institute of Arthritis and Musculoskeletal and Skin Diseases; Canadian Institutes of Health Research; Ottawa Hospital Research Institute","keywords":"Chromatin; Chromatin immunoprecipitation; ChIP-sequencing; Tandem affinity purification; Computational biology; DNA; DNA sequencing; Biology; Immunoprecipitation; Genome; ChIP-on-chip; ChIA-PET; Tandem; Molecular biology; Genetics; Affinity chromatography; Chromatin remodeling; Gene; Gene expression; Biochemistry; Promoter; Materials science","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":[0.0001546327,0.0001369645,0.0001081909,0.00002427135,0.00008757751,0.00007493622,0.0002418194,0.0004102215,0.00007020764],"category_scores_gemma":[0.00009407909,0.0001246051,0.00005990812,0.00007434847,0.00003037391,0.000005863293,0.00007216837,0.0002446291,0.00006808939],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004291393,"about_ca_system_score_gemma":0.0001028503,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000011763,"about_ca_topic_score_gemma":0.00001362948,"domain_scores_codex":[0.9991691,0.00003919865,0.0001952017,0.0002754135,0.0001215593,0.0001996022],"domain_scores_gemma":[0.9992812,0.000006666789,0.0001186965,0.0003925027,0.0001347556,0.00006623855],"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":[0.000005958783,0.00003220683,0.001594312,0.00003656895,0.00001621784,5.3577e-7,0.00002728017,0.00003594247,0.9921067,0.000429437,0.003555425,0.002159439],"study_design_scores_gemma":[0.00122467,0.0004250538,0.0315799,0.00009283714,0.00001372991,0.00003865697,0.0001193641,0.002573563,0.8916276,0.003990868,0.06763536,0.0006784626],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9559062,0.0001018469,0.0009842013,0.0002825178,0.00007046205,0.03669922,0.00001095132,0.00004302018,0.005901637],"genre_scores_gemma":[0.950965,0.000005084302,0.008329126,0.0003655948,0.0002217323,0.03952889,0.00009552154,0.00002433958,0.0004647438],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1004791,"threshold_uncertainty_score":0.5081249,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01048917005835851,"score_gpt":0.2714662106749797,"score_spread":0.2609770406166211,"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."}}