{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697376", "kind": "science-record", "revision": 8, "content_hash": "sha256:714cbaa534f1d7e523e9acc5905e95c933279d441440d9570fd4638d57bffd9d", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T22:42:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Assessment of microRNA expression in mouse epididymal epithelial cells and spermatozoa by next generation sequencing.", "doi": "10.1016/j.gdata.2015.09.012", "pmid": "26697376", "authors": ["Amanda L Anderson", "Simone J Stanger", "Bettina P Mihalas", "Sonika Tyagi", "Janet E Holt", "Eileen A McLaughlin", "Brett Nixon"], "journal": "Genomics data", "year": 2015, "abstract": "The mammalian epididymis is a highly specialized region of the male reproductive tract that is lined with a continuous layer of epithelial cells that display a remarkable level of regionalized secretory and absorptive activity. The luminal environment created by this combined secretory and absorptive activity is directly responsible for promoting the functional maturation of spermatozoa and their maintenance in a quiescent and viable state prior to ejaculation. This study was designed to identify the complement of microRNAs (miRNAs) that are expressed within the mouse epididymal epithelial cells and the maturing populations of spermatozoa. Through the use of Next Generation Sequencing technology we have demonstrated that both epididymal epithelial cells and spermatozoa harbour a complex repertoire of miRNAs that have substantially different expression profiles along the length of the tract. These data, deposited in the Gene Expression Omnibus (GEO) with the accession numbers GSE70197 and GSE70198, afford valuable insight into the post-transcriptional control of gene expression within the epididymis and provide the first evidence for the dynamic transformation of the miRNA content of maturing sperm cells. Ultimately such information promises to inform our understanding of the aetiology of male infertility. Herein we provide a detailed description of the methodology used to generate these important data.", "claims": [{"id": "claim-method", "statement": "Differential miRNA expression analysis was undertaken using R script based on, limma and voom libraries (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697376", "locator": "sections[9] \"miRNA Next-Generation Sequencing.\" paragraph 3", "quote": "Differential miRNA expression analysis was undertaken using R script based on, limma and voom libraries (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus [8] and are accessible through GEO Series accession number GSE70197 (epididymal tissue and epithelial cells miRNAs) and GSE70198 (epididymal spermatozoa miRNAs) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70197; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70198).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697376", "locator": "sections[9] \"miRNA Next-Generation Sequencing.\" paragraph 3", "quote": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus [8] and are accessible through GEO Series accession number GSE70197 (epididymal tissue and epithelial cells miRNAs) and GSE70198 (epididymal spermatozoa miRNAs) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70197; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70198)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study demonstrated that epididymal epithelial cells and spermatozoa contain complex miRNA repertoires with substantially different expression profiles along the epididymal tract. For the registered target, differential miRNA expression was analyzed using R scripts based on the limma and voom libraries, and the source data were deposited in GEO under accession numbers GSE70197 and GSE70198.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697376", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Through the use of Next Generation Sequencing technology we have demonstrated that both epididymal epithelial cells and spermatozoa harbour a complex repertoire of miRNAs that have substantially different expression profiles along the length of the tract."}, {"asset": "source:pmid:26697376", "locator": "sections[9] \"miRNA Next-Generation Sequencing.\" paragraph 3", "quote": "Differential miRNA expression analysis was undertaken using R script based on, limma and voom libraries (http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf)."}, {"asset": "source:pmid:26697376", "locator": "sections[9] \"miRNA Next-Generation Sequencing.\" paragraph 3", "quote": "The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus [8] and are accessible through GEO Series accession number GSE70197 (epididymal tissue and epithelial cells miRNAs) and GSE70198 (epididymal spermatozoa miRNAs) (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70197; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70198)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study demonstrated that epididymal epithelial cells and spermatozoa contain complex miRNA repertoires with substantially different expression profiles along the epididymal tract. For the registered target, differential miRNA expression was analyzed using R scripts based on the limma and voom libraries, and the source data were deposited in GEO under accession numbers GSE70197 and GSE70198.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26697376"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. 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Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}