Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34944421", "kind": "science-record", "revision": 2, "content_hash": "sha256:0bd5eb6d63b4b90f87b32a90c19746277657cc17beb9b1931646d336f87958d3", "created_at": "2026-11-01T17:36:39Z", "updated_at": "2026-11-01T18:57:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model.", "doi": "10.3390/biom11121776", "pmid": "34944421", "authors": ["Alicia Landeira-Viñuela", "Paula Díez", "Pablo Juanes-Velasco", "Quentin Lécrevisse", "Alberto Orfao", "Javier De Las Rivas", "Manuel Fuentes"], "journal": "Biomolecules", "year": 2021, "abstract": "Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that could provide insights into protein dynamics at the intracellular level. Here, 5672 unique proteins were systematically identified by MS/MS analysis and subcellular protein extraction strategies (neXtProt release 2020-21, MS/MS data are available via ProteomeXchange with identifier PXD003939). Moreover, RNA deep sequencing analysis of this lymphoma B-cell line identified 19,518 expressed genes and 5707 protein coding genes (mapped to neXtProt). Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization. Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles.", "claims": [{"id": "claim-data-access", "statement": "MS/MS data are available via ProteomeXchange with identifier PXD003939 at EBI-EMBL.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34944421", "locator": "sections[45] \"Data Availability Statement\" paragraph 2", "quote": "MS/MS data are available via ProteomeXchange with identifier PXD003939 at EBI-EMBL."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34944421", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization."}, {"asset": "source:pmid:34944421", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization.", "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:34944421"], "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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In the present study, using a B-cell", "model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomi", "gration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehe"], "order_basis": "paper_text_order:47", "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": ["d Cell Cultures—ECACC-Cat. no: 85030802) was cultured in RPMI 1640 medium supplemented with L-glutami"], "order_basis": "paper_text_order:1679", "id": "assay:2"}, {"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": ["usive proteins were determined. 2.9. Protein Microarray Data Processing Signal intensity values were", "MAP This study integrates multiplex antibody microarray detections (MAP) with subcellular protein lo", "ariants by SEC-MAP In the content of protein microarray, there are spotted antibodies targeting spec", ": List of protein target included in protein microarray. Table S3: Mapping of proteins with unique p"], "order_basis": "paper_text_order:6350", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ways are explored in the Ramos cell line: i. apoptosis regulation, ii. apoptosis inhibition, iii. B", "amos cell line: i. apoptosis regulation, ii. apoptosis inhibition, iii. BCR signaling pathway, iv."], "order_basis": "paper_text_order:7268", "id": "assay:4"}]}