Fig 1.
Study flowchart.
Table 1.
Patient characteristics for the analysis of granulosa cell gene expression associated with embryo quality.
Fig 2.
Hierarchical clustering and Differential Expression (DE) analysis of granulosa cells from good-quality (GQ) embryo transfer group compared with granulosa cells from poor-quality (PQ) embryo transfer group.
(A) A Venn diagram depicting the distribution of significant differentially expressed genes (DEGs) (fold change > 2.5, q <0.05) in our study. Numbers represent the number of different genes showing upregulated or downregulated expression in PQ embryo samples compared with GQ embryo samples with red representing upregulated expression and blue indicating downregulated expression. Numbers in parenthesis represent the number of DEGs in only PQ or GQ group. (B) Heatmap of the DEGs between the GQ and PQ embryo groups. The color key from blue to red represents the relative gene expression level from low to high, respectively. (C) Volcano plot showing DEG analysis between GQ embryo and PQ embryo groups using DESeq2; 640 genes were differentially expressed (210 downregulated (FC < -2 and FDR < 0.05) and 25 upregulated (FC > 2 and FDR < 0.05). The upregulated genes are represented using red dots; downregulated genes are denoted using blue dots; and the black dots indicate genes with no significant changes.
Fig 3.
Histogram of the Gene Ontology(GO) analysis of the differentially expressed genes (DEGs).
Genes were classified into three GO domains: biological process, cellular component, and molecular function. The left y-axis shows the gene count in each category. The solid columns indicate DEGs.
Fig 4.
Validation of RNAseq results using RT-qPCR of 13 targets normalized to GAPDH in duplicate.
Fold change was calculated using the 2ΔΔCt method between the good-quality (GQ) and poor-quality (PQ) embryos. *p <0.05. (A) Six genes associated with embryo quality both in our and previous studies. (B) Seven genes randomly selected from the NF-kB pathway.
Table 2.
Top 20 up-regulated genes in the poor-quality embryo transfer group compared with the good-quality embryo transfer group.
Table 3.
Top 20 downregulated genes in the poor-quality embryo transfer group compared with the good-quality embryo transfer group.
Table 4.
Candidate genes associated with embryo quality.