Differential expression runs with DESeq2 for coding sequences. Link to code.
This wasn’t the most interesting story. There are many DEGs, but appears to be mostly sex based. Super small number of differentially expressed DEGs when males and females are run separately. Continues to fit the story that most differences are sex-based. Can look at annotation to get a better idea of what the DEGs found actually are.
Combined Run
Volcano Plot
- 36242 significantly differentially expressed coding sequences
PCA - treatment
PCA - sex
PCA - treatment - labelled
PCA - sex - labelled
Top 50 Heatmap
- Clustered by sex
Female Run
Volcano Plot
- 25 significantly differentially expressed mRNAs
PCA - treatment
PCA - treatment - labelled
Top 50 Heatmap
- Clustered by treatment group
Male Run
Volcano Plot
- 107 significantly differentially expressed mRNAs
PCA - treatment
PCA - treatment - labelled
Top 50 Heatmap
- Clustered by treatment group except for one, view below:
