Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981420", "kind": "science-record", "revision": 5, "content_hash": "sha256:317e77e0af800ce4e86c3aeb845d79de912ca563bd9f153d46d0e68ccbc718dc", "created_at": "2026-11-01T15:40:17Z", "updated_at": "2026-11-01T18:48:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis.", "doi": "10.1016/j.gdata.2016.01.022", "pmid": "26981420", "authors": ["Kun Sun", "Liang Zhou", "Yu Zhao", "Huating Wang", "Hao Sun"], "journal": "Genomics data", "year": 2016, "abstract": "Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery and functional annotation of Linc-YY1, a novel lincRNA originating from the promoter of the transcription factor (TF) Yin Yang 1 (YY1). Starting from whole transcriptome shotgun sequencing (a.k.a. RNA-seq) data from muscle C2C12 cells, a series of bioinformatics analysis was applied towards the identification of hundreds of high-confidence novel lincRNAs. Genome-wide approaches were then employed to demonstrate that Linc-YY1 functions to promote myogenesis through associating with YY1 and regulating YY1/PRC2 transcriptional activity in trans. Here we describe the details of the ChIP-seq, RNA-seq experiments, and data analysis procedures associated with the study published by Zhou and colleagues in the Nature Communications Journal in 2015 Zhou et al. (2015) [1]. The data was deposited on NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE74049.", "claims": [{"id": "claim-data-access", "statement": "The data was deposited on NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE74049.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data was deposited on NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE74049."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Linc-YY1 promotes myogenesis by associating with YY1 and regulating YY1/PRC2 transcriptional activity in trans; protein–DNA binding peaks were identified with MACS v1.4.2 using IgG as background and a p-value cutoff of 10−5, and the source data are available from GEO under accession GSE74049.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Genome-wide approaches were then employed to demonstrate that Linc-YY1 functions to promote myogenesis through associating with YY1 and regulating YY1/PRC2 transcriptional activity in trans."}, {"asset": "source:pmid:26981420", "locator": "sections[6] \"Read alignment and peak calling\" paragraph 2", "quote": "The protein-DNA binding peaks were identified using Model-based Analysis for ChIP-seq (MACS [6], v1.4.2) with IgG control sample as background. The p-value cutoff was set as 10− 5 to call high-confidence binding sites."}, {"asset": "source:pmid:26981420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data was deposited on NCBI's Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE74049."}, {"asset": "source:pmid:26981420", "locator": "sections[2] \"Direct link to deposited data\" paragraph 1", "quote": "Direct link to deposited data"}, {"asset": "source:pmid:26981420", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74049."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Linc-YY1 promotes myogenesis by associating with YY1 and regulating YY1/PRC2 transcriptional activity in trans; protein–DNA binding peaks were identified with MACS v1.4.2 using IgG as background and a p-value cutoff of 10−5, and the source data are available from GEO under accession GSE74049.", "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:26981420"], "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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