We utilized DESeq2 to perform comparisons between groups of pseudobulk scRNA-seq samples in our healthy cohorts. Most of these comparisons were cross-sectional; that is, we used data from a single time point (Flu Year 1 Day 0) to compare age groups, CMV status groups, and biological sex groups. For the Flu Vaccine comparison, we performed comparisons between 7 days post-vaccination (Flu Year 1 Day 7) and the day of vaccine administration (Flu Year 1 Day 0) for all subjects with longitudinal collection across both time points.
In each case, we provide a "Foreground" and "Background" group designation. Differential expression results with positive log2(Fold Change) indicate higher expression in the "Foreground" group, while results with negative values indicate higher expression in the "Background" group.
| Comparison | scRNA-seq column | Background Group | Foreground Group |
|---|---|---|---|
| Age Group | cohort.cohortGuid |
BR1 (Young Adult) | BR2 (Older Adult) |
| Flu Vaccine | sample.visitName |
Flu Year 1 Day 0 | Flu Year 1 Day 7 |
| CMV Status | subject.cmv |
Negative | Positive |
| Biological Sex | subject.biologicalSex |
Female | Male |
For each comparison, we provide DESeq results for each cell type and gene. For additional details, see the Data Analysis Methods section. Descriptions of the columns in these results are available by clicking the header below.
DEG Results columnsAIFI_L3: Level 3 (high resolution) cell type used for differential expression testfg: Foreground group in the contrastbg: Background group in the contrastgene: Gene symbol for the contrast testlog2fc: Log2(Fold Change) of average expression between groups.padj: Adjusted P-value for the contrast test (using the Benjamini and Hochberg FDR method)pvalue: Original P-value generated by DESeq2 for the contrast teststat: Test statistic generated by DESeq2 for the contrast test
Sound Life Differential Gene Expression
| File Name | Description | Download Link |
|---|---|---|
| sound-life_age-group_deseq2-results_2025-02-07.csv | ||
| sound-life_biological-sex_deseq2-results_2025-02-07.csv | ||
| sound-life_cmv-status_deseq2-results_2025-02-07.csv | ||
| sound-life_flu-vaccine_deseq2-results_2025-02-07.csv |
2025-02-07: The differential expression test results files were found to contain only results from the Flu Vaccine comparison. These files have been corrected to include each of the contrasts indicated in their file names.