Transcriptomic analyses of primary astrocytes under TNFα treatment.

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Numerous studies suggested that astrocytes exhibit a functional and morphological high degree of plasticity. For example, following any brain injury, astrocytes become reactive and hypertrophic. This phenomenon, also called reactive gliosis, is characterized by a set of progressive gene expression and cellular changes [3]. Interestingly, in this context, astrocytes can re-acquire neurogenic properties. It has been shown that astrocytes can undergo dedifferentiation upon injury and inflammation, and may re-acquire the potentiality of neural progenitors [4], [5], [6], [7]. To assess the effect of inflammation on astrocytes, primary mouse astrocytes were treated with tumor necrosis factor α (TNFα), one of the main pro-inflammatory cytokines. The strength of this study is that pure primary astrocytes were used. As microglia are highly reactive immune cells, we used a magnetic cell sorting separation (MACS) method to further obtain highly pure astrocyte cultures devoid of microglia. Here, we provide details of the microarray data, which have been deposited in the Gene Expression Omnibus (GEO) under the series accession number GSE73022. The analysis and interpretation of these data are included in Gabel et al. (2015). Analysis of gene expression indicated that the NFκB pathway-associated genes were induced after a TNFα treatment. We have shown that primary astrocytes devoid of microglia can respond to a TNFα treatment with the re-expression of genes implicated in the glial cell development.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes between control and TNFα conditions were then determined using the empirical Bayes moderated t-statistic (eBayes) [11].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981349", "locator": "sections[5] \"Microarrays experiments, quality control and data analysis\" paragraph 3", "quote": "Differentially expressed genes between control and TNFα conditions were then determined using the empirical Bayes moderated t-statistic (eBayes) [11]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73022.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981349", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73022."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TNFα increases the expression of genes associated with the NFκB pathway and induces the re-expression of genes implicated in glial developmental processes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981349", "locator": "sections[6] \"Conclusion\" paragraph 3", "quote": "We show that TNFα increases the expression of genes associated with the NFκB pathway and induces the re-expression of genes implicated in glial developmental processes."}, {"asset": "source:pmid:26981349", "locator": "sections[5] \"Microarrays experiments, quality control and data analysis\" paragraph 3", "quote": "Differentially expressed genes between control and TNFα conditions were then determined using the empirical Bayes moderated t-statistic (eBayes) [11]."}, {"asset": "source:pmid:26981349", "locator": "sections[5] \"Microarrays experiments, quality control and data analysis\" paragraph 3", "quote": "P-value significance scores for these genes were adjusted for multiple hypotheses testing according to the Benjamini–Hochberg procedure [12]."}, {"asset": "source:pmid:26981349", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Here, we provide details of the microarray data, which have been deposited in the Gene Expression Omnibus (GEO) under the series accession number GSE73022."}, {"asset": "source:pmid:26981349", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73022."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TNFα increases the expression of genes associated with the NFκB pathway and induces the re-expression of genes implicated in glial developmental processes.", "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:26981349"], "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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