Figure 2

Global gene expression. A: Number of expressed genes. For each condition (stage x compartment) expressed genes are genes with an average expression >10 reads for ¾ of the replicates. Ubiquitous genes are genes expressed in all the samples. *: pval < 0.05 between PDO-PMO and SCO-SAO. B: Principal component analysis (PCA) of the transcriptome. PCA was performed on the gene data set after normalization using the R DEseq package. The first axis explains 52% of the expression variability and separates the two follicular compartments (O vs. GCs). The second axis explains 15% of the expression variability and separates the samples according to their follicular stages. C: Heatmap display of supervised hierarchical clustering of all the differential genes between compartments. The 1,694 genes are displayed in rows and the mean of replicates per condition are displayed in columns. Red, black and green represent up, mean, and down expression, respectively. D: Specific expression profiles. Relative quantification of BTG4 MCF2L, STA8SIA3 oocyte-specific genes and IFNE, ITIH5, DEFB112 GC-specific genes in the 2 follicular compartments and throughout early follicular development ((n = 3-4), Pd: primordial, Pm: primary, Sc: secondary, SA: small antrum). Expression specificity was checked by comparison with the expression of 3 amplified multi-tissue samples (3 independent pools of 12 tissues = MT) and non-amplified individual tissues. X axis from the left: PDO, PMO, SCO, SAO, PDG, PMG, SCG, SAG, MT1, MT2, MT3, fetal ovary, pituitary gland, hypothalamus, muscle, skin, hurt, lung, intestine, stomach, liver, kidney, spleen, fetal ovary, theca. The left Y axis corresponds to the relative expression normalized by 2 reference genes (Actin β and RPL19) from qPCR data (red color). The right Y axis corresponds to the normalized counts from RNA-seq data (blue color).