Comparative circRNA Profiling in Human Erythroblasts Derived from Fetal Liver and Bone Marrow Hematopoietic Stem Cells Using Public RNA-Seq Data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40943320", "kind": "science-record", "revision": 2, "content_hash": "sha256:13010d0ad0f0065b1cc897396bd782b9ae4d2312bb516514754886ed12bf7f57", "created_at": "2026-11-01T20:31:02Z", "updated_at": "2026-11-01T21:35:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative circRNA Profiling in Human Erythroblasts Derived from Fetal Liver and Bone Marrow Hematopoietic Stem Cells Using Public RNA-Seq Data.", "doi": "10.3390/ijms26178397", "pmid": "40943320", "authors": ["Alawi Habara"], "journal": "International journal of molecular sciences", "year": 2025, "abstract": "Circular RNAs (circRNAs) are increasingly recognized as regulators of gene expression, although their roles in hematopoietic differentiation remain relatively understudied. This study compares circRNA expression profiles between erythroblasts derived from human fetal liver and bone marrow CD34+ hematopoietic stem cells using publicly available RNA-seq datasets (GEO: GSE90878). Twelve samples from each developmental source were analyzed. Differential expression analysis was performed, and circAtlas 3.0 was employed to predict interactions between circRNAs, microRNAs (miRNAs), and RNA-binding proteins. Differentially expressed miRNAs were curated from miRNA-seq data (GEO: GSE110936) profiling the same cell types. Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R2 = 0.065). One circRNA, circALS2(4).1, was significantly upregulated in bone marrow-derived erythroblasts (adjusted p < 0.05), and ten additional circRNAs showed suggestive evidence for differential expression (adjusted p < 0.1). The resulting interaction networks reveal distinct circRNA landscapes and suggest regulatory circuits that may contribute to developmental differences in human erythropoiesis, indicating that the functions of circRNAs in hematopoietic development remain to be further elucidated.", "claims": [{"id": "claim-method", "statement": "Statistical significance was evaluated through non-parametric tests, and group-level differences were analyzed using PERMANOVA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40943320", "locator": "sections[13] \"4.3. Quantification and Differential Analysis\" paragraph 2", "quote": "Statistical significance was evaluated through non-parametric tests, and group-level differences were analyzed using PERMANOVA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed in this study are publicly available from the Gene Expression Omnibus (GEO) under accession numbers GSE90878 and GSE110936. The datasets can be accessed at https://www.ncbi.nlm.nih.gov/geo/ (accessed on 10 February 2025) using the provided accession numbers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40943320", "locator": "sections[26] \"notes\" paragraph 1", "quote": "All data analyzed in this study are publicly available from the Gene Expression Omnibus (GEO) under accession numbers GSE90878 and GSE110936. The datasets can be accessed at https://www.ncbi.nlm.nih.gov/geo/ (accessed on 10 February 2025) using the provided accession numbers."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using publicly available total RNA-seq data from GEO GSE90878, the paper found that principal component analysis of circRNA expression profiles showed significant separation between fetal liver- and bone marrow-derived erythroblasts, confirmed by PERMANOVA (p = 0.001), although the effect size was small (R2 = 0.065).", "kind": "quantitative", "target": {"value": 2.0, "unit": "correlation coefficient", "tolerance": null, "source": "Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R2 = 0.065)."}, "evidence": [{"asset": "source:pmid:40943320", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study compares circRNA expression profiles between erythroblasts derived from human fetal liver and bone marrow CD34+ hematopoietic stem cells using publicly available RNA-seq datasets (GEO: GSE90878)."}, {"asset": "source:pmid:40943320", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R2 = 0.065)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using publicly available total RNA-seq data from GEO GSE90878, the paper found that principal component analysis of circRNA expression profiles showed significant separation between fetal liver- and bone marrow-derived erythroblasts, confirmed by PERMANOVA (p = 0.001), although the effect size was small (R2 = 0.065).", "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:40943320"], "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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