Quantitative Proteomics After Spinal Cord Injury (SCI) in a Regenerative and a Nonregenerative Stage in the Frog Xenopus laevis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29358338", "kind": "science-record", "revision": 6, "content_hash": "sha256:4f204c84d28c4f7a72314db1742be001c3a3e9b6ba19e5ccb38088597d219513", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T21:21:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative Proteomics After Spinal Cord Injury (SCI) in a Regenerative and a Nonregenerative Stage in the Frog Xenopus laevis.", "doi": "10.1074/mcp.RA117.000215", "pmid": "29358338", "authors": ["Dasfne Lee-Liu", "Liangliang Sun", "Norman J Dovichi", "Juan Larraín"], "journal": "Molecular & cellular proteomics : MCP", "year": 2018, "abstract": "The capacity to regenerate the spinal cord after an injury is a coveted trait that only a limited group of nonmammalian organisms can achieve. In Xenopus laevis, this capacity is only present during larval or tadpole stages, but is absent during postmetamorphic frog stages. This provides an excellent model for comparative studies between a regenerative and a nonregenerative stage to identify the cellular and molecular mechanisms that explain this difference in regenerative potential. Here, we used iTRAQ chemistry to obtain a quantitative proteome of the spinal cord 1 day after a transection injury in regenerative and nonregenerative stage animals, and used sham operated animals as controls. We quantified a total of 6,384 proteins, with 172 showing significant differential expression in the regenerative stage and 240 in the nonregenerative stage, with an overlap of only 14 proteins. Functional enrichment analysis revealed that although the regenerative stage downregulated synapse/vesicle and mitochondrial proteins, the nonregenerative stage upregulated lipid metabolism proteins, and downregulated ribosomal and translation control proteins. Furthermore, STRING network analysis showed that proteins belonging to these groups are highly interconnected, providing interesting candidates for future functional studies. Data are available via ProteomeXchange with identifier PXD006993.", "claims": [{"id": "claim-method", "statement": "Welch's t test was selected in “Test,” using S0 = 0; Side = Both, and “p value” was selected in the “Use for truncation” option, with a 0.05 threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29358338", "locator": "sections[17] \"Protein Identification and Quantification\" paragraph 3", "quote": "Welch's t test was selected in “Test,” using S0 = 0; Side = Both, and “p value” was selected in the “Use for truncation” option, with a 0.05 threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE(41) partner repository with the dataset identifier PXD006993, available at: http://www.proteomexchange.org/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29358338", "locator": "sections[31] \"DATA AVAILABILITY\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE(41) partner repository with the dataset identifier PXD006993, available at: http://www.proteomexchange.org/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used a modified Welch’s t test with nominal p < 0.05 and an additional fold-change filter, and its quantitative proteome data are available through ProteomeXchange/PRIDE under PXD006993; at 1 day after injury, 172 proteins changed in the regenerative stage and 240 in the nonregenerative stage, with only 14 shared.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29358338", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we used iTRAQ chemistry to obtain a quantitative proteome of the spinal cord 1 day after a transection injury in regenerative and nonregenerative stage animals, and used sham operated animals as controls."}, {"asset": "source:pmid:29358338", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We quantified a total of 6,384 proteins, with 172 showing significant differential expression in the regenerative stage and 240 in the nonregenerative stage, with an overlap of only 14 proteins."}, {"asset": "source:pmid:29358338", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006993."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used a modified Welch’s t test with nominal p < 0.05 and an additional fold-change filter, and its quantitative proteome data are available through ProteomeXchange/PRIDE under PXD006993; at 1 day after injury, 172 proteins changed in the regenerative stage and 240 in the nonregenerative stage, with only 14 shared.", "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:29358338"], "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:PXD006993"], "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:PXD006993"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29358338", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.RA117.000215", "sha256": "sha256:3a0faef1bfb338ef3eac4f40b9753f1618e5287b16c6586f28941366e1b34b56", "bytes": 69115, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.RA117.000215", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5880103", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006993", "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=PXD006993", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006993", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE(41) partner repository with the dataset identifier PXD006993, available at: http://www.proteomexchange.org/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE(41) partner repository with the dataset identifier PXD006993, available at: http://www.proteomexchange.org/.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Quantitative proteomics after spinal cord injury in a regenerative and a non-regenerative stage in Xenopus laevis", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29358338:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:496cae16b40b07d38e277ab02e86fe38a0dad0a85cf4827f4efdf4c5bae650ff", "bytes": 1315, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[29]/table-wrap[1]#TI", "version": null, "note": "A comparison of the gene ontology (GO) categories enriched after spinal cord injury at the transcriptome (RNA-Seq) (8) and proteome (iTRAQ) levels. The total number of GO terms enriched among differentially expressed genes 1 day after injury, in the “biological process” and “cellular component” categories were included. A Venn diagram (not shown) was generated to determine which terms were enriched at both the RNA and protein levels, and which were only found in either analysis. Absolute number of terms (# terms) and percentages are included in the table (see Fig. 8 and supplementary Data S6 for additional information)", "structure": {"pmcid": "PMC5880103", "section_index": 29, "section_title": "A Comparative Analysis of Gene Ontologies Regulated at the Transcriptome and Proteome Level", "row_count": 7, "column_count": 9}, "table": {"label": "Table I", "caption": "A comparison of the gene ontology (GO) categories enriched after spinal cord injury at the transcriptome (RNA-Seq) (8) and proteome (iTRAQ) levels. The total number of GO terms enriched among differentially expressed genes 1 day after injury, in the “biological process” and “cellular component” categories were included. A Venn diagram (not shown) was generated to determine which terms were enriched at both the RNA and protein levels, and which were only found in either analysis. 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