Dataset Open Access
Alasoo, Kaur
<?xml version='1.0' encoding='utf-8'?> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#"> <rdf:Description rdf:about="https://doi.org/10.5281/zenodo.839011"> <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/> <dct:type rdf:resource="http://purl.org/dc/dcmitype/Dataset"/> <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.5281/zenodo.839011</dct:identifier> <foaf:page rdf:resource="https://doi.org/10.5281/zenodo.839011"/> <dct:creator> <rdf:Description> <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/> <foaf:name>Alasoo, Kaur</foaf:name> <foaf:givenName>Kaur</foaf:givenName> <foaf:familyName>Alasoo</foaf:familyName> <org:memberOf> <foaf:Organization> <foaf:name>Wellcome Trust Sanger Institute</foaf:name> </foaf:Organization> </org:memberOf> </rdf:Description> </dct:creator> <dct:title>Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection</dct:title> <dct:publisher> <foaf:Agent> <foaf:name>Zenodo</foaf:name> </foaf:Agent> </dct:publisher> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2017</dct:issued> <dcat:keyword>RNA-seq</dcat:keyword> <dcat:keyword>differential expression</dcat:keyword> <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2017-08-04</dct:issued> <owl:sameAs rdf:resource="https://zenodo.org/record/839011"/> <adms:identifier> <adms:Identifier> <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/839011</skos:notation> <adms:schemeAgency>url</adms:schemeAgency> </adms:Identifier> </adms:identifier> <dct:isVersionOf rdf:resource="https://doi.org/10.5281/zenodo.839010"/> <dct:isPartOf rdf:resource="https://zenodo.org/communities/macrophage-gene-expression-genetics"/> <dct:description><p>We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = “LRT”) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details: http://www.biorxiv.org/content/early/2017/05/18/102392 .</p> <p>We used the following commands in DESeq2:<br> #Run DESeq2<br> dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) <br> dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)</p> <p>#Extract differentially expressed genes in each condition<br> ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) <br> sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) <br> ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))</p></dct:description> <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/> <dct:accessRights> <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess"> <rdfs:label>Open Access</rdfs:label> </dct:RightsStatement> </dct:accessRights> <dcat:distribution> <dcat:Distribution> <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/> <dcat:accessURL rdf:resource="https://doi.org/10.5281/zenodo.839011"/> </dcat:Distribution> </dcat:distribution> <dcat:distribution> <dcat:Distribution> <dcat:accessURL>https://doi.org/10.5281/zenodo.839011</dcat:accessURL> <dcat:byteSize>1701488</dcat:byteSize> <dcat:downloadURL>https://zenodo.org/record/839011/files/naive_vs_IFNg_DESeq2_fold_change.txt.gz</dcat:downloadURL> <dcat:mediaType>text/plain</dcat:mediaType> </dcat:Distribution> </dcat:distribution> <dcat:distribution> <dcat:Distribution> <dcat:accessURL>https://doi.org/10.5281/zenodo.839011</dcat:accessURL> <dcat:byteSize>1694658</dcat:byteSize> <dcat:downloadURL>https://zenodo.org/record/839011/files/naive_vs_IFNg+Salmonella_DESeq2_fold_change.txt.gz</dcat:downloadURL> <dcat:mediaType>text/plain</dcat:mediaType> </dcat:Distribution> </dcat:distribution> <dcat:distribution> <dcat:Distribution> <dcat:accessURL>https://doi.org/10.5281/zenodo.839011</dcat:accessURL> <dcat:byteSize>1696396</dcat:byteSize> <dcat:downloadURL>https://zenodo.org/record/839011/files/naive_vs_Salmonella_DESeq2_fold_change.txt.gz</dcat:downloadURL> <dcat:mediaType>text/plain</dcat:mediaType> </dcat:Distribution> </dcat:distribution> </rdf:Description> </rdf:RDF>
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