Differential Gene Expression In Ipsc-Derived Macrophages After Ifng Stimulation And Salmonella Infection

Name: Differential Gene Expression In Ipsc-Derived Macrophages After Ifng Stimulation And Salmonella Infection
Creator: Zenodo
Published: 2020-09-18 22:03:43
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Zenodo2020-09-18 更新2026-05-25 收录

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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"))

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Zenodo

创建时间：

2017-08-04