{"id":"W2098357503","doi":"10.1371/journal.pone.0050226","title":"Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes","year":2012,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":229,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; University of Alberta; University of Toronto","funders":"National Institute on Drug Abuse; National Institute of Food and Agriculture; National Institutes of Health; University of Toronto; Max-Planck-Gesellschaft; University of Alberta; Western Canada Research Grid; Ministry of Advanced Education; National Science Foundation; Compute Canada; Universität zu Köln; Government of Alberta; Ministry of Advanced Education and Technology; Bill and Melinda Gates Foundation; Agency for Science, Technology and Research; Natural Sciences and Engineering Research Council of Canada; U.S. Department of Agriculture","keywords":"RNA; Biology; Transcriptome; Illumina dye sequencing; Deep sequencing; Computational biology; DNA sequencing; Genetics; Phylogenetic tree; RNA-Seq; Gene; Genome; Gene expression","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":[0.0008483917,0.000117834,0.0001852365,0.00001762761,0.0001745961,0.00001347488,0.0001017939,0.00006245814,0.000002782289],"category_scores_gemma":[0.0003324631,0.000091325,0.00005800688,0.00003673373,0.0000853266,0.000001767455,0.0001102918,0.0000556403,1.153975e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007661839,"about_ca_system_score_gemma":0.00002802932,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001546706,"about_ca_topic_score_gemma":0.000003620627,"domain_scores_codex":[0.9991263,0.000103533,0.0002255021,0.0001806192,0.000103722,0.0002603817],"domain_scores_gemma":[0.9994213,0.0001638674,0.0001072472,0.0001529462,0.0001012623,0.00005336029],"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":[0.00003523853,0.00006279457,0.03013542,0.00009704532,0.0002958156,3.405437e-8,0.0009022248,0.00004051372,0.9638947,0.00003798608,0.000001720529,0.004496465],"study_design_scores_gemma":[0.0004524924,0.0003716585,0.02136862,0.00005172345,0.0003185968,0.000004276559,0.0008042798,0.005814289,0.9705701,0.00007153898,0.00001890926,0.000153507],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9910319,0.004459517,0.003874659,0.00004333066,0.00006029836,0.0003446344,0.00005639405,0.00000291172,0.0001263705],"genre_scores_gemma":[0.8900955,0.0001406131,0.1094128,0.00003680262,0.0002326068,0.00004182649,0.000009007008,0.00001467728,0.00001615876],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1055382,"threshold_uncertainty_score":0.3724126,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1151025113604452,"score_gpt":0.3440252462852719,"score_spread":0.2289227349248267,"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."}}