Distinct microRNA expression profiles in follicle-associated epithelium and villous epithelium.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484293", "kind": "science-record", "revision": 5, "content_hash": "sha256:90e3d015606a8e7d877a6c9222c9adb1a0805b7f971418f83ae7febab3dd2d16", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T18:47:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Distinct microRNA expression profiles in follicle-associated epithelium and villous epithelium.", "doi": "10.1016/j.gdata.2015.07.011", "pmid": "26484293", "authors": ["Gaku Nakato", "Koji Hase", "Hiroshi Ohno"], "journal": "Genomics data", "year": 2015, "abstract": "M cells in follicle-associated epithelium (FAE) covering intestinal lymphoid follicles serve as a portal of entry for particulate antigens (Kanaya and Ohno, 2014 [1]). Despite their biological significance, molecular mechanisms that govern M-cell differentiation and function have not been fully elucidated. MicroRNAs (miRNAs) have a role to control host gene expression profiles that modulate cellular physiology and characteristic. Many studies have shown that miRNAs regulate diverse biological processes including developmental timing, differentiation and growth control of cells and tissues (Ivey and Srivastava, 2010 [2]). miRNAs are also relevant to differentiation and function of intestinal epithelium (McKenna et al., 2010 [3]; Runtsch et al., 2014 [4]). Expression profiles and functions of miRNAs in the intestinal epithelium have been examined in jejunal and colonic mucosa [3]. In contrast, those in FAE remain uncharacterized. To address this deficiency, we isolated Peyer's Patch (PP) FAE and villous epithelium (VE) surrounding the FAE, and compared the miRNA expression profiles of FAE and VE by microarray analysis. This revealed that 43 miRNAs were up-regulated, whereas 9 miRNAs were down-regulated, in FAE compared to VE. A unique pattern of miRNA expression by FAE may reflect important diversity in cellular phenotypes and/or functional features of FAE. All microarray data has been deposited at GEO under accession number GSE46264.", "claims": [{"id": "claim-data-access", "statement": "All microarray data has been deposited at GEO under accession number GSE46264.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484293", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All microarray data has been deposited at GEO under accession number GSE46264."}], "state": "complete"}, {"id": "claim-target-result", "statement": "No numerical result was reported specifically for the statistical method; expression differences were analyzed using Genespring version 11.0 with a two-fold significance threshold, and the source data were deposited at GEO under accession number GSE46264.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484293", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 2", "quote": "Data analysis was performed with Genespring software version 11.0 (Agilent Technologies). Two-fold expression difference between FAE and VE were considered to be significant."}, {"asset": "source:pmid:26484293", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All microarray data has been deposited at GEO under accession number GSE46264."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "No numerical result was reported specifically for the statistical method; expression differences were analyzed using Genespring version 11.0 with a two-fold significance threshold, and the source data were deposited at GEO under accession number GSE46264.", "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:26484293"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE46264"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE46264"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.07.011", "sha256": "sha256:cc15c14426d26d3c4451295e3c985231fb7dd738611eb4bfb6d30e6b2224342e", "bytes": 6518, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.07.011", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583698", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE46264", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46264", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46264", "version": null, "note": "All microarray data has been deposited at GEO under accession number GSE46264.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All microarray data has been deposited at GEO under accession number GSE46264.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1127859", "GSM1127860", "GSM1127861", "GSM1127862"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "10384", "taxon": "Mus musculus", "title": "Murine FAE and VE in BALB/cA mice", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484293:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9749f084d9fc0ff5ecd869b8f0deadf092256fabee6ff886b5b89b93bb06317b", "bytes": 1964, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "miRNAs upregulated more than 2-fold in the FAE as compared to VE.", "structure": {"pmcid": "PMC4583698", "section_index": 3, "section_title": "Experimental design, materials and methods", "row_count": 44, "column_count": 3}, "table": {"label": "Table 1", "caption": "miRNAs upregulated more than 2-fold in the FAE as compared to VE.", "rows": [["miRNA name", "miRBase accession number", "Fold change"], ["mmu-miR-15a*", "MIMAT0004624", "7.28"], ["mmu-miR-511", "MIMAT0004940", "5.69"], ["mmu-miR-872*", "MIMAT0004935", "5.16"], ["mmu-miR-582-3p", "MIMAT0005292", "4.51"], ["mmu-miR-193", "MIMAT0000223", "4.23"], ["mmu-miR-466d-3p", "MIMAT0004931", "3.95"], ["mmu-miR-365", "MIMAT0000711", "3.66"], ["mmu-miR-204", "MIMAT0000237", "3.47"], ["mmu-miR-149", "MIMAT0000159", "3.32"], ["mmu-miR-335-5p", "MIMAT0000766", "3.29"], ["mmu-miR-210", "MIMAT0000658", "3.22"], ["mmu-miR-18a*", "MIMAT0004626", "3.21"], ["mmu-miR-485*", "MIMAT0003129", "3.08"], ["mmu-miR-466 h", "MIMAT0004884", "3.01"], ["mmu-miR-452", "MIMAT0001637", "2.97"], ["mmu-miR-191*", "MIMAT0004542", "2.87"], ["mmu-miR-290-5p", "MIMAT0000366", "2.84"], ["mmu-miR-1224", "MIMAT0005460", "2.70"], ["mmu-miR-34a", "MIMAT0000542", "2.69"], ["mmu-miR-466a-3p", "MIMAT0002107", "2.69"], ["mmu-miR-335-3p", "MIMAT0004704", "2.68"], ["mmu-miR-1894-5p", "MIMAT0007877", "2.67"], ["mmu-miR-150", "MIMAT0000160", "2.62"], ["mmu-miR-297a*", "MIMAT0004864", "2.61"], ["mmu-miR-203*", "MIMAT0004547", "2.54"], ["mmu-miR-764-5p", "MIMAT0003894", "2.50"], ["mmu-miR-328", "MIMAT0000565", "2.43"], ["mmu-miR-296-5p", "MIMAT0000374", "2.42"], ["mmu-miR-669a", "MIMAT0003477", "2.42"], ["mmu-miR-206", "MIMAT0000239", "2.37"], ["mmu-miR-326", "MIMAT0000559", "2.36"], ["mmu-miR-346", "MIMAT0000597", "2.33"], ["mmu-miR-207", "MIMAT0000240", "2.29"], ["mmu-miR-211", "MIMAT0000668", "2.25"], ["mmu-miR-1196", "MIMAT0005857", "2.22"], ["mmu-miR-467 g", "MIMAT0005854", "2.20"], ["mmu-miR-467e*", "MIMAT0005294", "2.18"], ["mmu-miR-376b", "MIMAT0001092", "2.17"], ["mmu-miR-376a", "MIMAT0000740", "2.16"], ["mmu-miR-669 h-3p", "MIMAT0005842", "2.13"], ["mmu-miR-294", "MIMAT0000372", "2.09"], ["mmu-miR-672", "MIMAT0003735", "2.07"], ["mmu-miR-34b-3p", "MIMAT0004581", "2.06"]], "row_count": 44, "column_count": 3, "numeric_cells": 129, "header_rows": 1, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26484293:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:00e5331ccc753b4d5933997e4632ebe74eeefc121338d06cbb72d48ec4dd7ca4", "bytes": 618, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "miRNAs upregulated more than twice in the VE compared to the FAE.", "structure": {"pmcid": "PMC4583698", "section_index": 3, "section_title": "Experimental design, materials and methods", "row_count": 10, "column_count": 3}, "table": {"label": "Table 2", "caption": "miRNAs upregulated more than twice in the VE compared to the FAE.", "rows": [["miRNA name", "miRBase accession number", "Fold change"], ["mmu-miR-143", "MIMAT0000247", "16.31"], ["mmu-miR-451", "MIMAT0001632", "5.79"], ["mmu-miR-654-3p", "MIMAT0004898", "5.76"], ["mmu-miR-224", "MIMAT0000671", "2.92"], ["mmu-miR-10a", "MIMAT0000648", "2.34"], ["mmu-miR-219", "MIMAT0000664", "2.17"], ["mmu-miR-101a", "MIMAT0000133", "2.17"], ["mmu-miR-494", "MIMAT0003182", "2.07"], ["mmu-let-7e", "MIMAT0000524", "2.06"]], "row_count": 10, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:GSE46264 not downloaded", "asset:data:geo:GSE46264 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE46264"], "resolved_accessions": ["GSE46264"], "statements": ["All microarray data has been deposited at GEO under accession number GSE46264."], "basis": "The paper names GSE46264 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484293", "data:geo:GSE46264", "asset:table:pmid:26484293:1", "asset:table:pmid:26484293:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE46264"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:01Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 17166, "completion_tokens": 2096, "cached_tokens": 1688}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26484293", "type": "paper", "label": "pmid:26484293"}, {"id": "source:pmid:26484293", "type": "manuscript", "label": "PMID 26484293 full text"}, {"id": "data:geo:GSE46264", "type": "dataset", "label": "GEO GSE46264"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484293", "type": "paper", "label": "pmid:26484293"}, {"id": "source:pmid:26484293", "type": "manuscript", "label": "PMID 26484293 full text"}, {"id": "data:geo:GSE46264", "type": "dataset", "label": "GEO GSE46264"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484293", "type": "extraction", "used": ["source:pmid:26484293"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE46264", "type": "accession_resolution", "used": ["data:geo:GSE46264"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26484293", "parent_hash": "sha256:e3510caf375432ae6ed9ae65666e7ea1db8b94e8e80d5039850c47eeb0799060", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE46264 licence not read", "asset:data:geo:GSE46264 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e miRNA expression profiles of FAE and VE by microarray analysis. This revealed that 43 miRNAs were", "types and/or functional features of FAE. All microarray data has been deposited at GEO under accessi", "on profile was assessed by using Mouse miRNA Microarray Release 12.0 (Agilent Technologies). A hundr", "hed and then scanned with an Agilent G2565CA Microarray Scanner (Agilent Technologies). Data analysi"], "order_basis": "paper_text_order:1165", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["RNA expression profile was assessed by using Mouse miRNA Microarray Release 12.0 (Agilent Techn"], "order_basis": "paper_text_order:2138", "id": "assay:2"}]}