{"id":"W2205542261","doi":"10.1186/s12864-015-2264-z","title":"Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors","year":2016,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Reproductive Biology and Fertility","field":"Medicine","cited_by":47,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada; Academic Center for Education, Culture and Research; Royan Institute; Université Laval","keywords":"Reprogramming; Biology; Epigenetics; Somatic cell; Trichostatin A; Somatic cell nuclear transfer; Oocyte; Genetics; Computational biology; Transcriptome; Epigenomics; Epigenesis; DNA methylation; Cell; Embryo; Gene; Histone; Gene expression; Histone deacetylase; Embryogenesis","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":[0.0009861073,0.0002421911,0.0005004645,0.00007519629,0.0001716948,0.000006820497,0.0002745817,0.0002186332,0.00005229904],"category_scores_gemma":[0.0002337981,0.00009679366,0.0001950138,0.0002262173,0.0005844781,0.00004262137,0.00002268438,0.0002886563,0.00001540531],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001219124,"about_ca_system_score_gemma":0.0001339475,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000460175,"about_ca_topic_score_gemma":0.0001085322,"domain_scores_codex":[0.9980144,0.0002626748,0.0006686843,0.0005411776,0.0002263603,0.0002867375],"domain_scores_gemma":[0.9977855,0.0007475503,0.0002815801,0.0009467615,0.0001763889,0.00006219737],"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":[0.01603552,0.0001659057,0.01321072,0.0001899693,0.00009957478,0.000001567465,0.006735843,0.00004685829,0.9610635,0.00001114478,0.00003377706,0.002405619],"study_design_scores_gemma":[0.004118723,0.0003548029,0.2828336,0.00009341918,0.0002217663,0.00001478734,0.00188632,0.0002642245,0.7088027,0.00003309665,0.001203464,0.0001730842],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9915106,0.0006010879,0.004859368,0.001101434,0.0002323383,0.001518114,0.00008079562,0.00002815532,0.00006810194],"genre_scores_gemma":[0.99803,0.0002288483,0.001218973,0.00007197008,0.00006804046,0.00004017481,0.00002264757,0.0000414738,0.0002778413],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2696229,"threshold_uncertainty_score":0.3947131,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02840101213932628,"score_gpt":0.244839747213157,"score_spread":0.2164387350738307,"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."}}