Dataset Open Access
Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection
Alasoo, Kaur
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"))
| Name | Size | |
|---|---|---|
|
naive_vs_IFNg+Salmonella_DESeq2_fold_change.txt.gz
md5:5dfbed8bf82addcc42b8bba8f40f0a19 |
1.7 MB | Download |
|
naive_vs_IFNg_DESeq2_fold_change.txt.gz
md5:d30c466506cf7b6cb784ced7a9e4a68d |
1.7 MB | Download |
|
naive_vs_Salmonella_DESeq2_fold_change.txt.gz
md5:3fa2cf63753e72e1f5c884b9bcb1235c |
1.7 MB | Download |
| All versions | This version | |
|---|---|---|
| Views | 145 | 145 |
| Downloads | 48 | 50 |
| Data volume | 81.5 MB | 84.9 MB |
| Unique views | 138 | 138 |
| Unique downloads | 25 | 26 |
- Publication date:
- August 4, 2017
- DOI:
-
- Keyword(s):
- RNA-seq differential expression
- Communities:
- License (for files):
- Creative Commons Attribution 4.0 International