{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001179933,0.0007117474,0.0008905513,0.0009049079,0.0004720029,0.0007670558,0.0009350075,0.0003607599,0.003992418],"category_scores_gemma":[0.001358411,0.0007700323,0.0006425514,0.0008288868,0.0002775704,0.0003889181,0.0008690151,0.001049575,0.003785675],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003569441,"about_ca_system_score_gemma":0.0005312604,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005501715,"about_ca_topic_score_gemma":0.002377263,"domain_scores_codex":[0.9992825,0.00009742879,0.00007279626,0.0002143571,0.0002374035,0.00009554662],"domain_scores_gemma":[0.9992281,0.0001838454,0.0000591611,0.0001728603,0.0002415121,0.0001143963],"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":[0.000179315,0.0001019034,0.0007155505,0.0001646741,0.00004072026,0.0000639018,0.00007613862,0.001069757,0.9804105,0.00109353,0.0008782439,0.01520585],"study_design_scores_gemma":[0.00006751165,0.0002528853,0.005730445,0.00002762035,0.00008173414,0.0002163564,0.00004057424,0.01693708,0.942955,0.001146284,0.03248962,0.00005483604],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1179504,0.0008333984,0.8516789,0.0001377605,0.0001846125,0.001360277,0.01771315,0.005209645,0.004931791],"genre_scores_gemma":[0.2010816,0.001684635,0.6995187,0.0004514104,0.0001160671,0.003431424,0.07851391,0.001695591,0.01350662],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003992418,"threshold_uncertainty_score":0.01335591,"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."}}