{"id":"W2774801370","doi":"10.3791/56085","title":"Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis","year":2017,"lang":"en","type":"article","venue":"Journal of Visualized Experiments","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency","funders":"Terry Fox Research Institute; Canadian Institutes of Health Research; Genome British Columbia","keywords":"Nucleosome; Micrococcal nuclease; Chromatin immunoprecipitation; Histone code; Chromatin; Histone; Computational biology; ChIP-on-chip; ChIP-sequencing; Histone octamer; Biology; Genetics; Cell biology; DNA; Gene; Gene expression; Promoter","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":[0.0002578049,0.00009954179,0.0002686683,0.00008944926,0.0001892634,0.00008369438,0.000230736,0.00008045678,0.000008486767],"category_scores_gemma":[0.0001767555,0.00009282872,0.0002274119,0.00003939844,0.00005864269,0.00002876687,0.00006692242,0.00003613989,2.501181e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000396516,"about_ca_system_score_gemma":0.00009796194,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001266819,"about_ca_topic_score_gemma":0.000005601285,"domain_scores_codex":[0.9991583,0.00004538821,0.0004408203,0.0001152779,0.0001421902,0.00009806654],"domain_scores_gemma":[0.998212,0.00001215577,0.001177161,0.000241668,0.0003179116,0.00003904756],"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":[0.0001312748,0.00005417257,0.00110473,0.00001180291,0.0007476899,6.530904e-7,0.0007761273,0.0002514928,0.9963719,0.0002852968,0.00008295756,0.0001819651],"study_design_scores_gemma":[0.001098692,0.0003625083,0.004675836,0.00001627809,0.0001691327,0.000003893373,0.0004280619,0.006431899,0.9863396,0.000305807,0.00006919546,0.00009911034],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9747482,0.0003398546,0.02451756,0.00002189247,0.0001818392,0.0001107787,0.00001536174,0.000001436349,0.00006306089],"genre_scores_gemma":[0.9753773,0.00007175193,0.02425043,0.00002372052,0.0001496599,0.000004965172,0.00006035043,0.00001223398,0.00004959238],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01003225,"threshold_uncertainty_score":0.3785445,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0460680292182751,"score_gpt":0.3933561713593429,"score_spread":0.3472881421410678,"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."}}