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

Alasoo, Kaur

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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Alasoo, Kaur</dc:creator>
  <dc:date>2017-08-04</dc:date>
  <dc:description>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 .

We used the following commands in DESeq2:
#Run DESeq2
dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) 
dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)

#Extract differentially expressed genes in each condition
ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) 
sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) 
ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))</dc:description>
  <dc:identifier>https://zenodo.org/record/839011</dc:identifier>
  <dc:identifier>10.5281/zenodo.839011</dc:identifier>
  <dc:identifier>oai:zenodo.org:839011</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.839010</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/macrophage-gene-expression-genetics</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>RNA-seq</dc:subject>
  <dc:subject>differential expression</dc:subject>
  <dc:title>Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>
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Publication date:
August 4, 2017
DOI:
10.5281/zenodo.839011

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RNA-seq differential expression
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