Transcriptome comparison of distinct osteolineage subsets in the hematopoietic stem cell niche using a triple fluorescent transgenic mouse model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484277", "kind": "science-record", "revision": 4, "content_hash": "sha256:0d31118ff4eddd9f17282aeb591d0e2ce43408f6f1d98208d4e1e1e264f076a8", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T21:20:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome comparison of distinct osteolineage subsets in the hematopoietic stem cell niche using a triple fluorescent transgenic mouse model.", "doi": "10.1016/j.gdata.2015.06.001", "pmid": "26484277", "authors": ["Vionnie W C Yu", "Stefania Lymperi", "Francesca Ferraro", "David T Scadden"], "journal": "Genomics data", "year": 2015, "abstract": "The bone marrow niche is recognized as a central player in maintaining and regulating the behavior of hematopoietic stem and progenitor cells. Specific gain-of and loss-of function experiments perturbing a range of osteolineage cells or their secreted proteins had been shown to affect stem cell maintenance (Calvi et al, 2003 [1]; Stier et al., 2005 [2]; Zhang et al., 2003 [3]; Nilsson et al., 2005 [4]; Greenbaum et al., 2013 [5]) and engraftment (Adam et al., 2006, 2009 [6,7]). We used specific in vivo cell deletion approaches to dissect the niche cell-parenchymal cell dependency in a complex bone marrow microenvironment. Endogenous deletion of osteocalcin-expressing (Ocn(+)) cells led to a loss of T immune cells (Yu et al., 2015 [8]. Ocn(+) cells express the Notch ligand DLL4 to communicate with T-competent progenitors, and thereby ensuring T precursor production and expression of chemotactic molecules on their cell surface for subsequent thymic seeding. In contrast, depletion of osterix-expressing (Osx(+)) osteoprogenitors led to reduced B immune cells. These distinct hematopoietic phenotypes suggest specific pairing of mesenchymal niche cells and parenchymal hematopoietic cells in the bone marrow to create unique functional units to support hematopoiesis. Here, we present the global gene expression profiles of these osteolineage subtypes utilizing a triple fluorescent transgenic mouse model (OsxCre(+);Rosa-mCh(+);Ocn:Topaz(+)) that labels Osx(+) cells red, Ocn(+) cells green, and Osx(+) Ocn(+) cells yellow. This system allows isolation of distinct osteolineage subsets within the same animal by flow cytometry. Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042. Differences in gene expression may correlate with functional difference in supporting hematopoiesis.", "claims": [{"id": "claim-method", "statement": "Supervised learning or class prediction methods were used for molecular classification and pattern recognition.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484277", "locator": "sections[9] \"Differential expression quantification and classification\" paragraph 2", "quote": "Supervised learning or class prediction methods were used for molecular classification and pattern recognition."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484277", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used RMA normalization and supervised feature selection/class prediction to compare gene-expression profiles of Osx+ and Ocn+ osteolineage cells, with the source data available through GEO accession GSE66042.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484277", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we present the global gene expression profiles of these osteolineage subtypes utilizing a triple fluorescent transgenic mouse model (OsxCre+;Rosa-mCh+;Ocn:Topaz+) that labels Osx+ cells red, Ocn+ cells green, and Osx+ Ocn+ cells yellow."}, {"asset": "source:pmid:26484277", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042."}, {"asset": "source:pmid:26484277", "locator": "sections[8] \"Quality assessment\" paragraph 2", "quote": "The data was background corrected and normalized with RMA (Robust Multichip Average) using the “affy” BioConductor package."}, {"asset": "source:pmid:26484277", "locator": "sections[9] \"Differential expression quantification and classification\" paragraph 2", "quote": "Supervised learning or class prediction methods were used for molecular classification and pattern recognition."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used RMA normalization and supervised feature selection/class prediction to compare gene-expression profiles of Osx+ and Ocn+ osteolineage cells, with the source data available through GEO accession GSE66042.", "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:26484277"], "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:GSE66042"], "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:GSE66042"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484277", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.06.001", "sha256": "sha256:9e1362e794e3066832d735427caa37ad2695fe86a8800b22f273a9ad678daa4b", "bytes": 9121, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.06.001", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583650", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66042", "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=GSE66042", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66042", "version": null, "note": "Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1613452", "GSM1613453", "GSM1613454", "GSM1613455", "GSM1613456", "GSM1613457", "GSM1613458"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "8321", "taxon": "Mus musculus", "title": "Comparison of Osx+ cells and Ocn+ cells in the bone marrow.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26484277:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7313027fdd80e50a9bfee978e33f50226d5627735dea420d8d7bac32a4e921c7", "bytes": 942, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4583650", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Mus musculus"], ["Sex", "Females"], ["Sequencer or array type", "Affymetrix Mouse Genome 430A 2.0 Array"], ["Data format", "Raw data normalized"], ["Experimental factors", "Transcriptome comparison of Osx+ and Ocn+ osteolineage cells."], ["Experimental features", "In the OsxCre+;Rosa-mCh+;Ocn:Topaz+ mouse model, Osx+ cells were labeled red, Ocn+ cells were green, and Osx+ Ocn+ cells were yellow within the same animal. This system allows isolation of osteolineage subsets within the same animal by flow cytometry and subject to microarray comparison of global gene expression. Mice were 8–12 weeks old. Three replicates were used for each experimental condition."], ["Consent", "Allowed to reuse citing original author."], ["Sample source location", "NA"]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE66042 not downloaded", "asset:data:geo:GSE66042 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Supervised learning or class prediction methods", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Supervised learning or class prediction methods were used for molecular classification and pattern recognition."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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 (Supervised learning or class prediction methods), 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": ["GSE66042"], "resolved_accessions": ["GSE66042"], "statements": ["Array data that have been described in our study [8] are also publically available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE66042."], "basis": "The paper names GSE66042 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484277", "data:geo:GSE66042", "asset:table:pmid:26484277:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE66042"]}, "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": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 21048, "completion_tokens": 3014, "cached_tokens": 1824}}, "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:26484277", "type": "paper", "label": "pmid:26484277"}, {"id": "source:pmid:26484277", "type": "manuscript", "label": "PMID 26484277 full text"}, {"id": "data:geo:GSE66042", "type": "dataset", "label": "GEO GSE66042"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484277", "type": "paper", "label": "pmid:26484277"}, {"id": "source:pmid:26484277", "type": "manuscript", "label": "PMID 26484277 full text"}, {"id": "data:geo:GSE66042", "type": "dataset", "label": "GEO GSE66042"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484277", "type": "extraction", "used": ["source:pmid:26484277"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE66042", "type": "accession_resolution", "used": ["data:geo:GSE66042"], "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:26484277", "parent_hash": "sha256:27ded55ba8b492b6ef24e03c8e61a85dfdec776beeeaf47dd7ed4eebb13e19aa", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE66042 licence not read", "asset:data:geo:GSE66042 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["niche using a triple fluorescent transgenic mouse model.", "es utilizing a triple fluorescent transgenic mouse model (OsxCre(+);Rosa-mCh(+);Ocn:Topaz(+)) that la", "et al., 2006, 2009 [6,7]). We used specific in vivo cell deletion approaches to dissect the nich", "es utilizing a triple fluorescent transgenic mouse model (OsxCre(+);Rosa-mCh(+);Ocn:Topaz(+)) t"], "order_basis": "paper_text_order:89", "id": "assay:1"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["teolineage subsets within the same animal by flow cytometry. Array data that have been described in our"], "order_basis": "paper_text_order:1725", "id": "assay:2"}]}