Figure 1

Digital gene expression using RNA-seq. Differential gene expression was analyzed using the "DESeq" R package and plotted as a MA plot (a). Each point represents a gene (circle) or novel transcribed unit (triangle). The "M" axis is the log 2 fold change as compared to blastocyst and the "A" axis is the average log 2 normalized counts in the two samples. Red points indicate significant change as called by "DESeq" at FDR = 0.01. The two horizontal dashed lines marked the two-fold change thresholds. For comparison between RNA-seq and microarray, log 2 transformed RNA-seq and microarray gene expressions were plotted for blastocyst (b) and degenerative (c) respectively. Fold changes estimated using RNA-seq and microarrays were also compared (d).