Extended Data Fig. 2: OTX2 KD in human embryos on day 2.
From: Maternal factor OTX2 regulates human embryonic genome activation and early development
(a) Embryo developmental rates of control and OTX2 KD embryos from day 2 to day 4 from two independent batches. N, embryo numbers; MO, morula. (b) Volcano plot showing the differentially expressed genes upon OTX2 KD on D2. The x-axis and y-axis refer to the gene expression fold changes and the p-values computed by DESeq2, respectively. The up-regulated and down-regulated genes are marked in red and blue, respectively. (c) Heatmaps showing the single-embryo mRNA levels (FPKM followed by row z-score normalization) of DEGs upon OTX2 KD on day 2. (d) Violin plots showing the numbers of the OTX2 motif in nearby proximal or distal open chromatin regions for 4C-activated genes down-regulated and unaffected in OTX2 KD embryos on day 2. White center dot, median; black lines, 25th and 75th percentiles; whiskers, 1.5 × interquartile range; P-value, two-sided t-test, same for (i). (e) Immunostaining of TPRX1 in control and OTX2 KD embryos on day 2. Scale bar, 20 μm. (f) PCA of transcriptomes of FGO/MII/1C/2C/4C/8C/ICM (reference data)22, D2 control (black dots), and D2 OTX2 KD (red dots) embryos. (g) Box plots showing mRNA levels of maternal genes defined by Zou et al. that undergo decay at the 4C stage (4C FPKM/ 1C FPKM < 0.5) in normal development22, as well as in OTX2 KD and control embryos on day 2. Center line, median; box, 25th and 75th percentiles; whiskers, 1.5 × interquartile range. P-value, two-sided t-test. (h) Box plots showing the average mRNA levels of 4C-activated (top) and all expressed (bottom) genes in each D2 control and OTX2 KD embryos. The selected control and KD embryos of similar developmental stages are marked in blue and red, respectively. Center line, median; box, 25th and 75th percentiles; whiskers, 1.5 × interquartile range. (i) Violin plots showing the numbers of the OTX2 motif in nearby proximal or distal open chromatin regions for 4C-activated genes down-regulated and unaffected in OTX2 KD embryos selected from (h) on day 2. (j) Volcano plot showing the differentially expressed genes upon OTX2 KD in embryos selected from (h).
