Identification of transcripts regulated by CUG-BP, Elav-like family member 1 (CELF1) in primary embryonic cardiomyocytes by RNA-seq.

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Dysregulation of CELF1 has been implicated in cardiomyopathies in myotonic dystrophy type 1 and diabetes [2-5], but the targets of CELF1 regulation in the heart have not been systematically investigated. We previously demonstrated that in the developing heart CELF1 expression is restricted to the myocardium and peaks during embryogenesis [6-8]. To identify transcripts regulated by CELF1 in the embryonic myocardium, RNA-seq was used to compare the transcriptome of primary embryonic cardiomyocytes following siRNA-mediated knockdown of CELF1 to that of controls. Raw data files of the RNA-seq reads have been deposited in NCBI's Gene Expression Omnibus [9] under the GEO Series accession number GSE67360. These data can be used to identify transcripts whose levels or alternative processing (i.e., alternative splicing or polyadenylation site usage) are regulated by CELF1, and should provide insight into the pathways and processes modulated by this important RNA binding protein during normal heart development and during cardiac pathogenesis.", "claims": [{"id": "claim-method", "statement": "Statistical comparisons of means were performed via one-tailed t-tests assuming unequal variances using Microsoft Excel software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26366374", "locator": "sections[7] \"Validation of differential gene expression by real-time polymerase chain reaction\" paragraph 2", "quote": "Statistical comparisons of means were performed via one-tailed t-tests assuming unequal variances using Microsoft Excel software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data files of the RNA-seq reads have been deposited in NCBI's Gene Expression Omnibus [9], and are accessible through GEO Series accession number GSE67360.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26366374", "locator": "sections[6] \"RNA-seq and analysis\" paragraph 2", "quote": "Raw data files of the RNA-seq reads have been deposited in NCBI's Gene Expression Omnibus [9], and are accessible through GEO Series accession number GSE67360."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using CuffDiff with no effect-size cutoff and false-discovery-rate correction, the study identified 10,021 differentially expressed transcripts, and the raw RNA-seq reads are publicly available through GEO Series accession GSE67360.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26366374", "locator": "sections[6] \"RNA-seq and analysis\" paragraph 2", "quote": "Using no cutoff for the scale of differences, this identified 10,021 transcripts that differed between mock- and si2-transfected samples with P values ≤ 0.05 after correction for multiple testing and accounting for false discovery rate."}, {"asset": "source:pmid:26366374", "locator": "sections[6] \"RNA-seq and analysis\" paragraph 2", "quote": "Raw data files of the RNA-seq reads have been deposited in NCBI's Gene Expression Omnibus [9], and are accessible through GEO Series accession number GSE67360."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using CuffDiff with no effect-size cutoff and false-discovery-rate correction, the study identified 10,021 differentially expressed transcripts, and the raw RNA-seq reads are publicly available through GEO Series accession GSE67360.", "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:26366374"], "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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