Next-generation sequencing of microRNAs in primary human polarized macrophages.

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Small non-coding RNAs are important regulatory elements of gene expression and microRNAs are the most widely known to be fundamental for the proper development of cells of the immune system. Macrophages can exhibit different phenotypes, depending on the cytokine environment they encounter in the affected tissues. We have analyzed the microRNA expression profiles during maturation of human primary monocytes into macrophages and polarization by pro- or anti-inflammatory cytokines. Here we describe the analysis of next-generation sequencing data deposited in EMBL-EBI ArrayExpress under accession number E-MTAB-1969 and associated with the study published by Cobos Jiménez and collaborators in Physiological Genomics in 2014 (1). The data presented here contributes to our understanding of microRNA expression profiles in human monocytes and macrophages and will also serve as a resource for novel microRNAs and other small RNA species expressed in these cells.", "claims": [{"id": "claim-method", "statement": "To identify significantly expressed microRNAs between different stimulated cells compared with unstimulated macrophages or monocytes, all pairwise comparisons were analyzed using DESeq [10], a Bioconductor [11] package which uses a negative binomial distribution for statistical testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484091", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "To identify significantly expressed microRNAs between different stimulated cells compared with unstimulated macrophages or monocytes, all pairwise comparisons were analyzed using DESeq [10], a Bioconductor [11] package which uses a negative binomial distribution for statistical testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1969/", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484091", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found here: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1969/"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the DESeq Bioconductor package for statistical testing of differential microRNA expression, and the source sequencing data are available through EMBL–EBI ArrayExpress under accession number E-MTAB-1969.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484091", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "To identify significantly expressed microRNAs between different stimulated cells compared with unstimulated macrophages or monocytes, all pairwise comparisons were analyzed using DESeq [10], a Bioconductor [11] package which uses a negative binomial distribution for statistical testing."}, {"asset": "source:pmid:26484091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we describe the analysis of next-generation sequencing data deposited in EMBL–EBI ArrayExpress under accession number E-MTAB-1969 and associated with the study published by Cobos Jiménez and collaborators in Physiological Genomics in 2014 (1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the DESeq Bioconductor package for statistical testing of differential microRNA expression, and the source sequencing data are available through EMBL–EBI ArrayExpress under accession number E-MTAB-1969.", "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:26484091"], "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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