{"id":"W4301254839","doi":"10.3791/61124-v","title":"High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease (ChIP-Exo)","year":2020,"lang":"en","type":"article","venue":"Journal of Visualized Experiments","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Chromatin immunoprecipitation; Exonuclease; Exonuclease III; ChIP-sequencing; Immunoprecipitation; Biology; ChIP-on-chip; DNA; Chromatin; Molecular biology; Genomic library; DNA sequencing; Computational biology; Cell biology; Genetics; Gene; Gene expression; DNA polymerase; Chromatin remodeling; Escherichia coli; Promoter","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002870437,0.0003601882,0.0003775463,0.0005872821,0.000391467,0.0004609226,0.00036113,0.0003301024,0.001376835],"category_scores_gemma":[0.0001337507,0.0003026902,0.0004726469,0.0003644844,0.0003330269,0.0002761766,0.0004592415,0.0007978745,0.0007260252],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004046774,"about_ca_system_score_gemma":0.0004473675,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001697904,"about_ca_topic_score_gemma":0.006076915,"domain_scores_codex":[0.9997632,0.00001226337,0.00001480549,0.00009063177,0.00008160995,0.00003746917],"domain_scores_gemma":[0.9998941,0.0000253788,0.00002296902,0.00001525118,0.00001914282,0.00002301434],"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":[0.00001424368,0.00000592622,0.0001943152,0.00002539658,0.000004115949,0.00002368479,0.00001510216,0.00005872316,0.9981928,0.00009990707,0.00004052139,0.001325184],"study_design_scores_gemma":[0.000009015142,0.00004979553,0.01337006,0.00001328185,0.00002067889,0.000195901,0.00004532253,0.001444588,0.9799075,0.0002433233,0.00469122,0.000009327972],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8148928,0.003847849,0.1649363,0.0003187303,0.00009802372,0.0001999302,0.006368657,0.00156426,0.007773473],"genre_scores_gemma":[0.7819663,0.00392978,0.1888326,0.0003382154,0.0000228566,0.0006003561,0.008032967,0.0005040548,0.01577296],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001697904,"threshold_uncertainty_score":0.004606009,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03062718526789373,"score_gpt":0.3729726182878657,"score_spread":0.342345433019972,"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."}}