Dataset Open Access

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

Alasoo, Kaur


Citation Style Language JSON Export

{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.839011", 
  "title": "Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection", 
  "issued": {
    "date-parts": [
      [
        2017, 
        8, 
        4
      ]
    ]
  }, 
  "abstract": "<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>", 
  "author": [
    {
      "family": "Alasoo, Kaur"
    }
  ], 
  "type": "dataset", 
  "id": "839011"
}
40
13
views
downloads
All versions This version
Views 4040
Downloads 1313
Data volume 22.1 MB22.1 MB
Unique views 3939
Unique downloads 66

Share

Cite as