Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy.

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We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation. Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE64507.", "claims": [{"id": "claim-method", "statement": "We found a significant loss of nucleosome occupancy at the 4 h time point post S. typhimurium stimulation (K-S test 2.2 × 10− 16) (Fig. 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484165", "locator": "sections[8] \"Detection of nucleosome occupancy dynamics during the immune response\" paragraph 2", "quote": "We found a significant loss of nucleosome occupancy at the 4 h time point post S. typhimurium stimulation (K-S test 2.2 × 10− 16) (Fig. 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Illumina Hi-Seq 2500 data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64507.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484165", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Illumina Hi-Seq 2500 data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64507."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper found significant genome-wide nucleosome loss at 4 h after Salmonella typhimurium stimulation, with a reported K-S test value of 2.2 × 10− 16, and deposited the Illumina Hi-Seq 2500 source data in GEO under GSE64507.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484165", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation."}, {"asset": "source:pmid:26484165", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE64507."}, {"asset": "source:pmid:26484165", "locator": "sections[8] \"Detection of nucleosome occupancy dynamics during the immune response\" paragraph 2", "quote": "We found a significant loss of nucleosome occupancy at the 4 h time point post S. typhimurium stimulation (K-S test 2.2 × 10− 16) (Fig. 1)."}, {"asset": "source:pmid:26484165", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Illumina Hi-Seq 2500 data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64507."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper found significant genome-wide nucleosome loss at 4 h after Salmonella typhimurium stimulation, with a reported K-S test value of 2.2 × 10− 16, and deposited the Illumina Hi-Seq 2500 source data in GEO under GSE64507.", "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:26484165"], "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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