839011
doi
10.5281/zenodo.839011
oai:zenodo.org:839011
user-macrophage-gene-expression-genetics
Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection
Alasoo, Kaur
Wellcome Trust Sanger Institute
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
RNA-seq
differential expression
<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>
Zenodo
2017-08-04
info:eu-repo/semantics/other
839010
user-macrophage-gene-expression-genetics
1579893864.321818
1701488
md5:d30c466506cf7b6cb784ced7a9e4a68d
https://zenodo.org/records/839011/files/naive_vs_IFNg_DESeq2_fold_change.txt.gz
1694658
md5:5dfbed8bf82addcc42b8bba8f40f0a19
https://zenodo.org/records/839011/files/naive_vs_IFNg+Salmonella_DESeq2_fold_change.txt.gz
1696396
md5:3fa2cf63753e72e1f5c884b9bcb1235c
https://zenodo.org/records/839011/files/naive_vs_Salmonella_DESeq2_fold_change.txt.gz
public
10.5281/zenodo.839010
isVersionOf
doi