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Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection

Alasoo, Kaur


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{
  "description": "<p>We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = \u201cLRT\u201d) 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:\u00a0http://www.biorxiv.org/content/early/2017/05/18/102392 .</p>\n\n<p>We used the following commands in DESeq2:<br>\n#Run DESeq2<br>\ndds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name)\u00a0<br>\ndds = DESeq2::DESeq(dds, test = \"LRT\", reduced = ~ 1)</p>\n\n<p>#Extract differentially expressed genes in each condition<br>\nifng_genes = results(dds, contrast=c(\"condition_name\",\"IFNg\",\"naive\"))\u00a0<br>\nsl1344_genes = results(dds, contrast=c(\"condition_name\",\"SL1344\",\"naive\"))\u00a0<br>\nifng_sl1344_genes = results(dds, contrast=c(\"condition_name\",\"IFNg_SL1344\",\"naive\"))</p>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Wellcome Trust Sanger Institute", 
      "@type": "Person", 
      "name": "Alasoo, Kaur"
    }
  ], 
  "url": "https://zenodo.org/record/839011", 
  "datePublished": "2017-08-04", 
  "keywords": [
    "RNA-seq", 
    "differential expression"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_IFNg_DESeq2_fold_change.txt.gz", 
      "@type": "DataDownload", 
      "fileFormat": "gz"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_IFNg+Salmonella_DESeq2_fold_change.txt.gz", 
      "@type": "DataDownload", 
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_Salmonella_DESeq2_fold_change.txt.gz", 
      "@type": "DataDownload", 
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  ], 
  "identifier": "https://doi.org/10.5281/zenodo.839011", 
  "@id": "https://doi.org/10.5281/zenodo.839011", 
  "@type": "Dataset", 
  "name": "Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection"
}
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