Proteomic data of the Trypanosoma cruzi insect-dwelling epimastigotes overexpressing the RNA-binding protein UBP1.

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The role of this regulatory protein during the epimastigote-to-metacyclic trypomastigote stage transition was clearly established by our group at the transcriptome level; nevertheless, the impact of UBP1 overexpression on protein synthesis is not known. To address this question, we performed shotgun label-free quantification proteomics using an in vitro system based on the tetracycline-inducible expression of TcUBP1 and epimastigote wildtype cells. Using tryptic peptide digestion and LC-MS/MS analysis with Orbitrap technology, this data file describes the proteome of three biological samples per condition and yields 1637 correctly quantified proteins. The statistical comparisons of the two analyzed groups within the Proteome Discoverer platform identified 379 differentially expressed proteins, with 207 being up-regulated and 172 being down-regulated. In addition, profile plots and heatmap analysis to visualize the distribution of protein abundances within replicates are also presented. Data are available via ProteomeXchange with identifier PXD047761.", "claims": [{"id": "claim-data-access", "statement": "Proteomic data of the Trypanosoma cruzi RNA-binding protein UBP1 induction and knockdown in insect-dwelling epimastigotes (Original data) (PRIDE).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38348324", "locator": "sections[17] \"Data Availability\" paragraph 2", "quote": "Proteomic data of the Trypanosoma cruzi RNA-binding protein UBP1 induction and knockdown in insect-dwelling epimastigotes (Original data) (PRIDE)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The statistical comparison identified 379 differentially expressed proteins in UBP1-overexpressing versus control epimastigotes, including 207 up-regulated and 172 down-regulated proteins.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38348324", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The statistical comparisons of the two analyzed groups within the Proteome Discoverer platform identified 379 differentially expressed proteins, with 207 being up-regulated and 172 being down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The statistical comparison identified 379 differentially expressed proteins in UBP1-overexpressing versus control epimastigotes, including 207 up-regulated and 172 down-regulated proteins.", "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:38348324"], "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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