Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697387", "kind": "science-record", "revision": 8, "content_hash": "sha256:e328ace915ce57cddda70a06b12af2e052b1ded2f7204b16c8b29b5972f0079b", "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": "Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model.", "doi": "10.1016/j.gdata.2015.10.005", "pmid": "26697387", "authors": ["Benjamin J Harrison", "Gayathri Venkat", "Thomas Hutson", "Kristofer K Rau", "Mary Bartlett Bunge", "Lorne M Mendell", "Fred H Gage", "Richard D Johnson", "Caitlin Hill", "Eric C Rouchka", "Lawrence Moon", "Jeffrey C Petruska"], "journal": "Genomics data", "year": 2015, "abstract": "Primary afferent collateral sprouting is a process whereby non-injured primary afferent neurons respond to some stimulus and extend new branches from existing axons. Neurons of both the central and peripheral nervous systems undergo this process, which contributes to both adaptive and maladaptive plasticity (e.g., [1], [2], [3], [4], [5], [6], [7], [8], [9]). In the model used here (the \"spared dermatome\" model), the intact sensory neurons respond to the denervation of adjacent areas of skin by sprouting new axon branches into that adjacent denervated territory. Investigations of gene expression changes associated with collateral sprouting can provide a better understanding of the molecular mechanisms controlling this process. Consequently, it can be used to develop treatments to promote functional recovery for spinal cord injury and other similar conditions. This report includes raw gene expression data files from microarray experiments in order to study the gene regulation in spared sensory ganglia in the initiation (7 days) and maintenance (14 days) phases of the spared dermatome model relative to intact (\"naïve\") sensory ganglia. Data has been deposited into GEO (GSE72551).", "claims": [{"id": "claim-method", "statement": "Differential expression was performed using Limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697387", "locator": "sections[7] \"Data acquisition\" paragraph 2", "quote": "Differential expression was performed using Limma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is available through the Gene Expression Omnibus (GEO) [10] through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72551", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697387", "locator": "sections[3] \"Direct link to deposited data\" paragraph 2", "quote": "Data is available through the Gene Expression Omnibus (GEO) [10] through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72551"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using RMA and Limma, the analysis identified 917 differentially expressed probe sets at day 7 versus naïve and 1,920 at day 14 versus naïve, defined by fold-change ≥ 1.2 with p-value < 0.05; the raw gene expression data were deposited in GEO under accession GSE72551.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Analysis of the data using RMA and Limma results in 917 differentially expressed probe sets at day 7 vs. naïve and 1920 differentially expressed probe sets at day 14 vs. naïve, as defined by fold-change > = 1.2 with p-value < 0.05."}, "evidence": [{"asset": "source:pmid:26697387", "locator": "sections[8] \"Results\" paragraph 2", "quote": "Analysis of the data using RMA and Limma results in 917 differentially expressed probe sets at day 7 vs. naïve and 1920 differentially expressed probe sets at day 14 vs. naïve, as defined by fold-change > = 1.2 with p-value < 0.05."}, {"asset": "source:pmid:26697387", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data has been deposited into GEO (GSE72551)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using RMA and Limma, the analysis identified 917 differentially expressed probe sets at day 7 versus naïve and 1,920 at day 14 versus naïve, defined by fold-change ≥ 1.2 with p-value < 0.05; the raw gene expression data were deposited in GEO under accession GSE72551.", "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:26697387"], "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:GSE72551"], "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:GSE72551"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26697387", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.10.005", "sha256": "sha256:456f792db79d412c0ba0fcd49b72ad20ede193124ba024129ad2c25650543906", "bytes": 10673, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.10.005", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4664766", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE72551", "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=GSE72551", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72551", "version": null, "note": "Data is available through the Gene Expression Omnibus (GEO) [10] through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72551", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available through the Gene Expression Omnibus (GEO) [10] through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72551", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1865032", "GSM1865033", "GSM1865034", "GSM1865035", "GSM1865036", "GSM1865037", "GSM1865038", "GSM1865039", "GSM1865040", "GSM1865041", "GSM1865042", "GSM1865043", "GSM1865044", "GSM1865045", "GSM1865046", "GSM1865047", "GSM1865048", "GSM1865049", "GSM1865050"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "1355", "taxon": "Rattus norvegicus", "title": "Transcriptional changes in sensory ganglion associated with primary afferent collateral sprouting in spared dermatome model", "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:26697387:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4f8975ed1566f650d4d41e058bc0adb8767f5ac05c21daba17d8b8b4199eb7ba", "bytes": 807, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC4664766", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Rattus norvegicus"], ["Sex", "Female"], ["Sequencer or array type", "Affymetrix GeneChip microarray Rattus norvegicus 230_2"], ["Data format", "Raw; CEL files"], ["Experimental factors", "T11 spared DRG, day 7 post injury vs. naïve; T11 spared DRG, day 14 post injury vs. naïve"], ["Experimental features", "Gene expression profiling of the T11 spared dermatome using naïve rats (n = 5), T11 spared DRG at day 7 post denervation of neighboring dermatomes (n = 7), and T11 spared DRG at day 14 post denervation of neighboring dermatomes (n = 7)"], ["Consent", "Not applicable"], ["Sample source location", "Not applicable"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:26697387:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4f8975ed1566f650d4d41e058bc0adb8767f5ac05c21daba17d8b8b4199eb7ba", "bytes": 807, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC4664766", "section_index": 2, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Rattus norvegicus"], ["Sex", "Female"], ["Sequencer or array type", "Affymetrix GeneChip microarray Rattus norvegicus 230_2"], ["Data format", "Raw; CEL files"], ["Experimental factors", "T11 spared DRG, day 7 post injury vs. naïve; T11 spared DRG, day 14 post injury vs. naïve"], ["Experimental features", "Gene expression profiling of the T11 spared dermatome using naïve rats (n = 5), T11 spared DRG at day 7 post denervation of neighboring dermatomes (n = 7), and T11 spared DRG at day 14 post denervation of neighboring dermatomes (n = 7)"], ["Consent", "Not applicable"], ["Sample source location", "Not applicable"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0015"}}], "gaps": ["asset:data:geo:GSE72551 not downloaded", "asset:data:geo:GSE72551 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential expression was performed using Limma."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE72551"], "resolved_accessions": ["GSE72551"], "statements": ["Data is available through the Gene Expression Omnibus (GEO) [10] through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72551"], "basis": "The paper names GSE72551 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26697387", "data:geo:GSE72551", "asset:table:pmid:26697387:1", "asset:table:pmid:26697387:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE72551"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:55Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 24638, "completion_tokens": 2558, "cached_tokens": 1312}}, "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:26697387", "type": "paper", "label": "pmid:26697387"}, {"id": "source:pmid:26697387", "type": "manuscript", "label": "PMID 26697387 full text"}, {"id": "data:geo:GSE72551", "type": "dataset", "label": "GEO GSE72551"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26697387", "type": "paper", "label": "pmid:26697387"}, {"id": "source:pmid:26697387", "type": "manuscript", "label": "PMID 26697387 full text"}, {"id": "data:geo:GSE72551", "type": "dataset", "label": "GEO GSE72551"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26697387", "type": "extraction", "used": ["source:pmid:26697387"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE72551", "type": "accession_resolution", "used": ["data:geo:GSE72551"], "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:26697387", "parent_hash": "sha256:7a35d189f7aec69bf4aadab2543cc4f5632c910b661bbdd066a63f001978f3dc", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE72551 licence not read", "asset:data:geo:GSE72551 not downloaded", "execution.not_run", "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": ["includes raw gene expression data files from microarray experiments in order to study the gene regul", "ed onto microarrays. Each animal had its own microarray with T11 DRG mRNA sample which underwent 2-r", "dy using whole DRG homogenate. A total of 20 Affymetrix Rat Genome 230 2.0 microarrays were analyzed", "d and hybridized to Rat 230 2.0 microarrays (Affymetrix) according to manufacturer's instructions."], "order_basis": "paper_text_order:1013", "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": 0.99, "evidence": ["l segment (T11). Adult female Sprague–Dawley rats (260–310 g) were anesthetized with pentobarb", "h expansion barely-detectible in some of the rats by 7 days, but easily detectible in all rats", "rats by 7 days, but easily detectible in all rats by 14 days. Temporal progression of this pro", "ole DRG homogenate. A total of 20 Affymetrix Rat Genome 230 2.0 microarrays were analyzed: si"], "order_basis": "paper_text_order:2126", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differential expression was performed using Limma."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}