Data on microRNA expression, predicted gene targets and pathway analysis in response to different concentrations of a cranberry proanthocyanidin-rich extract and its metabolite 3-(4-hydroxyphenyl)-propionic acid in intestinal Caco-2BBe1 cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38516278", "kind": "science-record", "revision": 3, "content_hash": "sha256:f4b1fbd1ee13136eec69099eeac444d337b278a98caf1989e70f7b77349e4db3", "created_at": "2026-11-01T19:20:27Z", "updated_at": "2026-11-01T21:32:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data on microRNA expression, predicted gene targets and pathway analysis in response to different concentrations of a cranberry proanthocyanidin-rich extract and its metabolite 3-(4-hydroxyphenyl)-propionic acid in intestinal Caco-2BBe1 cells.", "doi": "10.1016/j.dib.2024.110238", "pmid": "38516278", "authors": ["Zoe Dimoff", "Zoe Lofft", "Fred Liang", "Siying Chen", "Paraskevi Massara", "Diana Wu", "Inke Paetau-Robinson", "Christina Khoo", "Amel Taibi", "Elena M Comelli"], "journal": "Data in brief", "year": 2024, "abstract": "Cranberry-derived proanthocyanidin (PAC) is processed by the gut microbiota to produce 3-(4-hydroxyphenyl)-propionic acid (HPPA), among other metabolites. These data are in support of the article entitled, \"Cranberry proanthocyanidin and its microbial metabolite 3,4-dihydroxyphenylacetic acid, but not 3-(4-hydroxyphenyl)-propionic acid, partially reverse pro-inflammatory microRNA responses in human intestinal epithelial cells,\" published in Molecular Nutrition and Food Research [1]. Here we describe data generated by nCounterⓇ Human v3 miRNA Expression Panel of RNA obtained from Caco-2BBe1 cells exposed to two different concentrations of cranberry extract rich in PAC (50 µg/ml or 100 µg/ml) or 3-(4-hydroxyphenyl)-propionic acid (5 µg/ml or 10 µg/ml) for 24 h, then stimulated with 1 ng/ml of IL-1ß or not (mock) for three hours. The raw data are publicly available at the NCBI GEO database GSE237078. This work also includes descriptive methodological procedures, treatment-responsive microRNA (miRNA) expression profiles in Caco-2BBe1 cells, and in silico mRNA gene target and pathway enrichment analyses of significantly differentially expressed miRNAs (q < 0.001). Cranberry and its components have recognized health benefits, particularly in relation to combatting inflammation and pathogenic bacterial adhesion. These data will be valuable as a reference to study the response of intestinal cells to other polyphenol-rich food sources, analyze gut microbial responses to cranberry and its metabolites in different cell lines and mammalian hosts to elucidate individualized effects, and to delineate the role of the gut microbiota in facilitating the benefits of cranberry. Moreover, these data will aid in expanding our knowledge on the mechanisms underlying the benefits of cranberry and its components.", "claims": [{"id": "claim-method", "statement": "The processing and statistical analysis of the raw data were performed in R version 3.51 and R version 4.2.1 [2], using the R packages NanostringDiff, NanostringNorm, and Pheatmap [3], [4], [5].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38516278", "locator": "sections[7] \"RNA extraction and miRNA profiling\" paragraph 2", "quote": "The processing and statistical analysis of the raw data were performed in R version 3.51 and R version 4.2.1 [2], using the R packages NanostringDiff, NanostringNorm, and Pheatmap [3], [4], [5]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "miRNA expression data (Original data) (NCBI GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38516278", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "miRNA expression data (Original data) (NCBI GEO)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:38516278"], "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:GSE237078"], "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:GSE237078"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38516278", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2024.110238", "sha256": "sha256:99a02e5f284a0175ef31f2610de33ea5b30f286f985cac412623bbd4db7bc9da", "bytes": 17341, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2024.110238", "version": null, "note": "Full article fetched from PMC; 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