Global analysis of CPSF2-mediated alternative splicing: Integration of global iCLIP and transcriptome profiling data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697379", "kind": "science-record", "revision": 7, "content_hash": "sha256:a407091a318f826e6253937da1679ec8a0d35e9384d3a452b773b8f98e42a549", "created_at": "2026-11-01T15:40:15Z", "updated_at": "2026-11-01T21:58:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Global analysis of CPSF2-mediated alternative splicing: Integration of global iCLIP and transcriptome profiling data.", "doi": "10.1016/j.gdata.2015.09.022", "pmid": "26697379", "authors": ["Ashish Misra", "Jianhong Ou", "Lihua Julie Zhu", "Michael R Green"], "journal": "Genomics data", "year": 2015, "abstract": "Alternative splicing is a key mechanism for generating proteome diversity, however the mechanisms regulating alternative splicing are poorly understood. Using a genome-wide RNA interference screening strategy, we identified cleavage and polyadenylation specificity factor (CPSF) and symplekin (SYMPK) as cofactors of the well-known splicing regulator RBFOX2. To determine the role of CPSF in alternative splicing on a genome-wide level, we performed paired-end RNA sequencing (RNA-seq) to compare splicing events in control cells and RBFOX2 or CPSF2 knockdown cells. We also performed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to identify direct binding targets of RBFOX2 and CPSF2. Here, we describe the experimental design, and the quality control and data analyses that were performed on the dataset. The raw sequencing data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE60392.", "claims": [{"id": "claim-method", "statement": "Alternative splicing events were identified using the DEXSeq (v1.10.6) package, which models the exon counts as the negative binomial distribution and uses generalized linear models to test differential exon-usage using variance estimated from biological replicates [6].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697379", "locator": "sections[7] \"High-throughput sequencing and bioinformatic analysis of RNA-seq data\" paragraph 3", "quote": "Alternative splicing events were identified using the DEXSeq (v1.10.6) package, which models the exon counts as the negative binomial distribution and uses generalized linear models to test differential exon-usage using variance estimated from biological replicates [6]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw sequencing data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE60392.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697379", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw sequencing data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE60392."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found that CPSF along with SYMPK promotes alternative splicing at internal introns and exons; statistically, alternative splicing was analyzed with DEXSeq using negative-binomial models and generalized linear models, and the iCLIP and RNA-seq source data are available through GEO accession GSE60392.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697379", "locator": "sections[8] \"Discussion\" paragraph 2", "quote": "Our results show that CPSF along with SYMPK is involved in promoting alternative splicing at internal introns and exons and shed light on a new role of mRNA 3′ end formation factors [4]."}, {"asset": "source:pmid:26697379", "locator": "sections[7] \"High-throughput sequencing and bioinformatic analysis of RNA-seq data\" paragraph 3", "quote": "Alternative splicing events were identified using the DEXSeq (v1.10.6) package, which models the exon counts as the negative binomial distribution and uses generalized linear models to test differential exon-usage using variance estimated from biological replicates [6]."}, {"asset": "source:pmid:26697379", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The iCLIP and RNA-seq data are available at the following GEO series: GSE60392, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60392."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study found that CPSF along with SYMPK promotes alternative splicing at internal introns and exons; statistically, alternative splicing was analyzed with DEXSeq using negative-binomial models and generalized linear models, and the iCLIP and RNA-seq source data are available through GEO accession GSE60392.", "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:26697379"], "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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We also performed individual-nucleoti", "length of 100 bp for duplicated NS, RBFOX2- knockdown and CPSF2-knockdown samples. The quality of", "r duplicated NS, RBFOX2- knockdown and CPSF2-knockdown samples. The quality of the sequencing reads", "and dissimilarity among NS, RBFOX2 and CPSF2 knockdown samples using cummeRbund package (v 2.8.2) ["], "order_basis": "paper_text_order:624", "id": "assay:2"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Pearson correlation"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}