1*B* | Gene counts for differential expression analysis | Moderated *t* tests with linear regression (empirical Bayes) | FDR < 0.1 | limma Bioconductor package: voom approach |

1*C* | Gene set enrichment analysis | Hypergeometric test | FDR < 0.05 | clusterProfiler Bioconductor package: compareClusters approach |

1*D* | Normalized qPCR data | Student's *t* test | *p* < 0.05 | |

2*B* | Normalized qPCR data | Student's *t* test | *p* < 0.05 | |

2*C* | Gene counts for differential expression analysis | Moderated *t* tests with linear mixed effects modeling (empirical Bayes) | Bonferroni < 0.05 | limma Bioconductor package: voom approach |

2*D* | Gene set enrichment analysis | Hypergeometric test | FDR < 0.05 | clusterProfiler Bioconductor package: compareClusters approach |

2*E* | Normalized qPCR data | Student's *t* test | *p* < 0.05 | |

3*B* | Normalized qPCR data | Student's *t* test | *p* < 0.05 | |

3*C* | Differential expression analysis | Moderated *t* tests with linear regression (empirical Bayes) | FDR < 0.05 | limma Bioconductor package: voom approach |

3*D* | GO enrichment analysis | Hypergeometric test | FDR < 0.05 | clusterProfiler Bioconductor package: compareClusters approach |

4*A* | Normalized qPCR data | Student's *t* test | *p* < 0.05 | |

4*B* | Normally distributed | Student's *t* test | *p* < 0.05 | |