Microglia specific alternative splicing alterations in multiple sclerosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39115871", "kind": "science-record", "revision": 3, "content_hash": "sha256:897f8b4aeba53476e63894fc0ca02a1ab5b7e8e76b0d977675c9d12ad31246f9", "created_at": "2026-11-01T20:29:12Z", "updated_at": "2026-11-01T22:12:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microglia specific alternative splicing alterations in multiple sclerosis.", "doi": "10.18632/aging.206045", "pmid": "39115871", "authors": ["Caiyun Qi", "Honglei Ren", "Yong Fan"], "journal": "Aging", "year": 2024, "abstract": "Several aberrant alternative splicing (AS) events and their regulatory mechanisms are widely recognized in multiple sclerosis (MS). Yet the cell-type specific AS events have not been extensively examined. Here we assessed the diversity of AS events using web-based RNA-seq data of sorted CD15-CD11b+ microglia in white matter (WM) region from 10 patients with MS and 11 control subjects. The GSE111972 dataset was downloaded from GEO and ENA databases, aligned to the GRCh38 reference genome from ENSEMBL via STAR. rMATS was used to assess five types of AS events, alternative 3'SS (A3SS), alternative 5'SS (A5SS), skipped exon (SE), retained intron (RI) and mutually exclusive exons (MXE), followed by visualizing with rmats2sashimiplot and maser. Differential genes or transcripts were analyzed using the limma R package. Gene ontology (GO) analysis was performed with the clusterProfiler R package. 42,663 raw counts of AS events were identified and 132 significant AS events were retained based on the filtered criteria: 1) average coverage >10 and 2) delta percent spliced in (ΔPSI) >0.1. SE was the most common AS event (36.36%), followed by MXE events (32.58%), and RI (18.94%). Genes related to telomere maintenance and organization primarily underwent SE splicing, while genes associated with protein folding and mitochondrion organization were predominantly spliced in the MXE pattern. Conversely, genes experiencing RI were enriched in immune response and immunoglobulin production. In conclusion, we identified microglia-specific AS changes in the white matter of MS patients, which may shed light on novel pathological mechanisms underlying MS.", "claims": [{"id": "claim-method", "statement": "After STAR process, we used the sorted bam files for AS analysis via rMATs v4.0.2 and then visualized them by rmats2sashiplot.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39115871", "locator": "sections[6] \"Alternative splicing analysis\" paragraph 2", "quote": "After STAR process, we used the sorted bam files for AS analysis via rMATs v4.0.2 and then visualized them by rmats2sashiplot."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset GSE111972 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111972) was obtained from the Gene Expression Omnibus (GEO) database. 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All data generated in the current study can be found in the article and Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using rMATS on the GSE111972 RNA-seq data, the study identified 42,663 raw AS events and retained 132 significant AS events.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39115871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSE111972 dataset was downloaded from GEO and ENA databases, aligned to the GRCh38 reference genome from ENSEMBL via STAR."}, {"asset": "source:pmid:39115871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "rMATS was used to assess five types of AS events, alternative 3’SS (A3SS), alternative 5’SS (A5SS), skipped exon (SE), retained intron (RI) and mutually exclusive exons (MXE), followed by visualizing with rmats2sashimiplot and maser."}, {"asset": "source:pmid:39115871", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "42,663 raw counts of AS events were identified and 132 significant AS events were retained based on the filtered criteria: 1) average coverage >10 and 2) delta percent spliced in (ΔPSI) >0.1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using rMATS on the GSE111972 RNA-seq data, the study identified 42,663 raw AS events and retained 132 significant AS events.", "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:39115871"], "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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