Anti-inflammatory cytokine stimulation of HMC3 cells: Proteome dataset.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37554993", "kind": "science-record", "revision": 1, "content_hash": "sha256:1a78ce65d797fd9271a7c25035210198b36522acde54e6fe85bb00bea4932a45", "created_at": "2026-11-01T19:02:20Z", "updated_at": "2026-11-01T19:02:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Anti-inflammatory cytokine stimulation of HMC3 cells: Proteome dataset.", "doi": "10.1016/j.dib.2023.109433", "pmid": "37554993", "authors": ["Shreya Ahuja", "Iulia M Lazar"], "journal": "Data in brief", "year": 2023, "abstract": "The immunoprotective functions of microglia in the brain are mediated by the inflammatory M1 phenotype. This phenotype is challenged by anti-inflammatory cytokines which polarize the microglia cells to an immunosuppressive M2 phenotype, a trait that is often exploited by cancer cells to evade immune recognition and promote tumor growth. Investigating the molecular determinants of this behavior is crucial for advancing the understanding of the mechanisms that cancer cells use to escape immune attack. In this article, we describe liquid chromatography (LC)-mass spectrometry (MS)/proteomic data acquired with an EASY-nanoLC 1200-Q ExactiveTM OrbitrapTM mass spectrometer that reflect the response of human microglia cells (HMC3) to stimulation with potential cancer-released anti-inflammatory cytokines known to be key players in promoting tumorigenesis in the brain (IL-4, IL-13, IL-10, TGFB and MCP-1). The MS files were processed with the Proteome Discoverer v.2.4 software package. The cell culture conditions, the sample preparation protocols, the MS acquisition parameters, and the data processing approach are described in detail. The RAW and processed MS files associated with this work were deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the dataset identifiers PXD023163 and PXD023166, and the analyzed data in the Mendeley Data cloud-based repository with DOI 10.17632/fvhw2zwt5d.1. The biological interpretation of the data can be accessed in the research article \"Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-inflammatory Cytokines\" (Shreya Ahuja and Iulia M. Lazar, Frontiers in Immunology 2021 [1]). The proteome data described in this article will benefit researchers who are either interested in re-processing the data with alternative search engines and filtering criteria, and/or exploring the data in more depth to advance the understanding of cancer progression and the discovery of novel biomarkers or drug targets.", "claims": [{"id": "claim-data-access", "statement": "Proteomic analysis of human microglia cells (HMC3) stimulated with anti-inflammatory cytokines using serum-deprived culture conditions (Original data) (PRIDE)Proteomic analysis of human microglia cells (HMC3) stimulated with anti-inflammatory cytokines using serum-enriched culture conditions (Original data) (PRIDE)Anti-Inflammatory Cytokine Stimulation of HMC3 Cells: Proteome Dataset (Original data) (Mendeley Data)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37554993", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "Proteomic analysis of human microglia cells (HMC3) stimulated with anti-inflammatory cytokines using serum-deprived culture conditions (Original data) (PRIDE)Proteomic analysis of human microglia cells (HMC3) stimulated with anti-inflammatory cytokines using serum-enriched culture conditions (Original data) (PRIDE)Anti-Inflammatory Cytokine Stimulation of HMC3 Cells: Proteome Dataset (Original data) (Mendeley Data)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:37554993"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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MS/RAW Data Processing The RAW mass spectrometry files were interpreted with the Proteome Dis", "d chromatography (LC)-mass spectrometry (MS)/proteomic data acquired with an EASY-nanoLC 1200-Q Exa", "essed in the research article \"Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Su"], "order_basis": "paper_text_order:588", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["(IL-4, IL-10, IL-13, CCL2, TGFβ1/TGFβ2-both HEK293 derived) were purchased from Peprotech (Rock"], "order_basis": "paper_text_order:2486", "id": "assay:2"}, {"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": ["y Hill, NJ). 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