Analysis of different expression RNA binding protein genes in mouse microglia cell from the brains of mice 72 h after subarachnoid hemorrhage or sham operation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39095742", "kind": "science-record", "revision": 4, "content_hash": "sha256:bb417924c820e1eb209eef2e479565f77b62a909e28ec5105cab1624b430471f", "created_at": "2026-11-01T20:29:10Z", "updated_at": "2026-11-01T22:54:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of different expression RNA binding protein genes in mouse microglia cell from the brains of mice 72 h after subarachnoid hemorrhage or sham operation.", "doi": "10.1186/s12920-024-01972-x", "pmid": "39095742", "authors": ["Xinyi Pan", "Hengyang Ouyang", "Xue Xiao", "Xiaobing Zhou", "Lingfeng Lai"], "journal": "BMC medical genomics", "year": 2024, "abstract": "BACKGROUND: The prognosis of brain injury caused by subarachnoid hemorrhage (SAH) is poor. Previous studies showed that abnormal function of RBPs might be involved in brain injury, neuroinflammation and further affect microglia homeostasis. However, no studies have systematically analyzed the genome-wide abnormal expression of RBPs genes in microglia during SAH.\nMETHODS: RNA-seq data of microglia from the SAH mouse group (SAH) and control sham-operated mouse group (sham) were downloaded from the GEO database in GSE167957, including four samples from the sham group and four samples from the SAH group for subsequent analysis.Utilizing GO and KEGG functional enrichment analyses, we conducted a comprehensive study of differentially expressed genes (DEGs), alternative splicing patterns, and co-expression networks to gain deeper insights into the differential expression of RNA-binding proteins (RBPs) and differential alternative splicing events (ASEs) between the SAH (subarachnoid hemorrhage) and sham groups. This analysis aimed to elucidate the potential mechanisms underlying the aberrant expression of RBPs in microglia during brain injury caused by SAH.\nRESULTS: ASEs and co-expression analyses of differentially expressed RBPs and differential ASEs were carried out in microglia in terms of gene expression. GO and KEGG functional enrichment analysis showed that aberrantly expressed RBPs such as Mcm7, Mtdh, SRSF3, and Hnrnpa2b1 may affect and regulate downstream Csnk1d, Uckl1 and other protein phosphorylation-related genes by alterative splicing.\nCONCLUSION: RBPs were aberrantly expressed in microglia during the development of brain injury secondary to SAH, regulating alterative splicing of downstream genes and influencing the progression of SAH brain injury in this study. This implies that RBPs are important for the identification of new therapeutic targets for brain injury after SAH.", "claims": [{"id": "claim-method", "statement": "For performing the analysis of differential gene expression, the software DEseq2 is opted [17].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39095742", "locator": "sections[4] \"Analysis of differentially expressed genes (DEG) and read alignment\" paragraph 2", "quote": "For performing the analysis of differential gene expression, the software DEseq2 is opted [17]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Public data were analyzed in this project. All data can be colocted from KEGG (http://www.genome.jp/kegg) and GEO databases (http://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39095742", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "Public data were analyzed in this project. All data can be colocted from KEGG (http://www.genome.jp/kegg) and GEO databases (http://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential expression analysis identified 1,198 differentially expressed genes between SAH and sham microglia, including 879 upregulated and 319 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39095742", "locator": "sections[11] \"Analysis of gene expression profile of microglia from mouse with SAH\" paragraph 2", "quote": "And gene differential expression analysis showed that there were 1198 differential expression genes, including 879 genes upregulation, 319 genes downregulation, between SAH and Sham group, which indicated microglial gene abnormal expression (Fig. 1B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential expression analysis identified 1,198 differentially expressed genes between SAH and sham microglia, including 879 upregulated and 319 downregulated genes.", "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:39095742"], "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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METHODS: RNA-seq data of microglia from the SAH mouse group (", "e right panel, the quantification of ASEs by RNA-seq is displayed. The formula alternative splice", "determine the changing ratio of AS events in RNA-seq. 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