Proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32055664", "kind": "science-record", "revision": 8, "content_hash": "sha256:f06c2a2da9f6c50699a762044fdcb087c3c8eb14d5b2b6ae5b1193622e7bdf66", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T22:44:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages.", "doi": "10.1016/j.dib.2020.105179", "pmid": "32055664", "authors": ["Turan Demircan", "Mustafa Sibai", "Ebru Altuntaş"], "journal": "Data in brief", "year": 2020, "abstract": "The presented data article reports protein expression profiles during a time course of limb regeneration in the highly regenerative neotenic and regeneration-deficient metamorphic axolotl (Ambystoma mexicanum). A protein database was first generated from transcriptome data, which was used concomitantly with nanoLC-MS/MS to identify and assess significant changes of protein levels among 0, 1, 4, and 7 days post-amputation (dpa) in both animal stages, yielding a total of 714 significant differentially expressed proteins. Gene ontology categories of these identified proteins were examined in terms of biological processes, molecular function and cellular components. Innate clustering patterns of the samples were investigated using hierarchical clustering and were visualized on a heatmap. The data reported here constitutes an extension of \"Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl\" article Sibai et al., 2019 [1]. The associated mass spectrometry raw data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) with the dataset identifier PXD014806.", "claims": [{"id": "claim-method", "statement": "Significance level among groups were calculated by ANOVA method and resulting dataset with p-value ≤ 0.01 were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32055664", "locator": "sections[8] \"LC-MS/MS data processing\" paragraph 3", "quote": "Significance level among groups were calculated by ANOVA method and resulting dataset with p-value ≤ 0.01 were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data related to this article were deposited to the:1-) ProteomeXchangeRepository name: PRIDEData identification number: PXD014806Direct URL to data: https://www.ebi.ac.uk/pride/archive/projects/PXD0148062-) FigshareRepository name: FigshareData identification number: 10.6084/m9.figshare.11492319Direct URL to data: https://figshare.com/s/b5049269e4384ce8ec3b", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32055664", "locator": "sections[1] \"table-wrap\" paragraph 1", "quote": "Data related to this article were deposited to the:1-) ProteomeXchangeRepository name: PRIDEData identification number: PXD014806Direct URL to data: https://www.ebi.ac.uk/pride/archive/projects/PXD0148062-) FigshareRepository name: FigshareData identification number: 10.6084/m9.figshare.11492319Direct URL to data: https://figshare.com/s/b5049269e4384ce8ec3b"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32055664"], "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:PXD014806"], "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:PXD014806"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32055664", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2020.105179", "sha256": "sha256:5b20acd46be46d0fa0f8f832eb701b697b0c6f7d3ce60eef30aac58980d6df54", "bytes": 20147, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2020.105179", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7005509", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD014806", "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=PXD014806", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD014806", "version": null, "note": "Data related to this article were deposited to the:1-) ProteomeXchangeRepository name: PRIDEData identification number: PXD014806Direct URL to data: https://www.ebi.ac.uk/pride/archive/projects/PXD0148062-) FigshareRepository name: FigshareData identification number: 10.6084/m9.figshare.11492319Direct URL to data: https://figshare.com/s/b5049269e4384ce8ec3b", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data related to this article were deposited to the:1-) ProteomeXchangeRepository name: PRIDEData identification number: PXD014806Direct URL to data: https://www.ebi.ac.uk/pride/archive/projects/PXD0148062-) FigshareRepository name: FigshareData identification number: 10.6084/m9.figshare.11492319Direct URL to data: https://figshare.com/s/b5049269e4384ce8ec3b", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparison of Protein Expression During Early Phases of Limb Regeneration Between Regeneration-permissive and Regeneration-deficient Axolotl", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD014806 not downloaded", "asset:data:geo:PXD014806 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Significance level among groups were calculated by ANOVA method and resulting dataset with p-value ≤ 0.01 were considered statistically significant."}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "hierarchical clustering"}}], "targets": [], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD014806"], "resolved_accessions": ["PXD014806"], "statements": ["Data related to this article were deposited to the:1-) ProteomeXchangeRepository name: PRIDEData identification number: PXD014806Direct URL to data: https://www.ebi.ac.uk/pride/archive/projects/PXD0148062-) FigshareRepository name: FigshareData identification number: 10.6084/m9.figshare.11492319Direct URL to data: https://figshare.com/s/b5049269e4384ce8ec3b"], "basis": "The paper names PXD014806 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:32055664", "data:geo:PXD014806"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD014806"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 16688, "completion_tokens": 2235, "cached_tokens": 793}}, "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:32055664", "type": "paper", "label": "pmid:32055664"}, {"id": "source:pmid:32055664", "type": "manuscript", "label": "PMID 32055664 full text"}, {"id": "data:geo:PXD014806", "type": "dataset", "label": "GEO PXD014806"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32055664", "type": "paper", "label": "pmid:32055664"}, {"id": "source:pmid:32055664", "type": "manuscript", "label": "PMID 32055664 full text"}, {"id": "data:geo:PXD014806", "type": "dataset", "label": "GEO PXD014806"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32055664", "type": "extraction", "used": ["source:pmid:32055664"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD014806", "type": "accession_resolution", "used": ["data:geo:PXD014806"], "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:32055664", "parent_hash": "sha256:717d2a439faf1617e9dfc59329e6dbe3d39236a98e6fb0c272855ee6280d2af2", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD014806 licence not read", "asset:data:geo:PXD014806 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ticle Sibai et al., 2019 [1]. The associated mass spectrometry raw data have been deposited in the Proteome", "ls were used for sample preparation prior to LC-MS/MS [7]. UPX protein extraction buffer (Expedeon", "digest the protein lysate for 18 h. Prior to LC-MS/MS analysis, Quantitative Fluorometric Peptide", "employed to measure peptide concentrations. LC-MS/MS data processing To analyze the peptide featu"], "order_basis": "paper_text_order:1053", "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": ["analyses) was created with the corresponding mouse orthologues and their gene symbols (Suppleme"], "order_basis": "paper_text_order:7324", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Significance level among groups were calculated by ANOVA method and resulting dataset with p-value ≤ 0.01 were considered statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}