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Genome-wide differential expression analysis

MC Minghao Chia
CL Cai Li
SM Sueli Marques
VP Vicente Pelechano
NL Nicholas M. Luscombe
FW Folkert J. van Werven
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Differential expression analysis was performed with the DESeq2 package (version 1.18.1) [93] in R (version 3.4.1). The raw read counts of called TSS/TES clusters, which are required input for running DESeq2, were extracted from aforementioned coverage tracks by bigWigAverageOverBed [94]. The clusters with log2(fold change) > =1 and padj < 0.05 in the DESeq2 results were considered as significantly differentially expressed clusters.

Each time point corresponding to early gametogenesis (SPO 3–6 h) was compared to pre-meiotic cells immediately prior to IME1 induction (SPO 2 h). Each time point corresponding to mid-late gametogenesis (SPO 7–9 h) was compared to cells in meiotic prophase, prior to NDT80 induction (SPO 6 h). The SPO 3M starvation controls were compared to pre-meiotic cells at SPO 2 h. The SPO 7M starvation controls were compared to meiotic prophase cells at SPO 6 h.

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