Fig. 3

Transcriptome analysis and signaling pathway validation after Lr-pgrn-s1 knockdown in embryonic cells. A Heatmap showing the expression of 100 genes in the control and experimental groups. Color intensity indicates expression levels. The color scale adjacent to the heatmap indicates the raw Z-score, ranging from green (low expression) to red (high expression). The similarity between individuals with hierarchical clustering is shown above the heatmap. B Volcano plot of differentially expressed genes (DEGs) between the experimental and control groups. DEGs with p-value < 0.05 and |log₂ FC| > 2 were screened. One dot indicates one gene, red dots represent upregulated genes, green dots represent downregulated genes, and black dots indicate undifferentiated genes in the volcano. The smaller the q-value, the larger the −log(q-value), and the more significant the gene differentially expressed between the experimental and control groups. C, D GO analysis of the transcriptomic data of Lr-pgrn-s1knockdown of embryonic cells. The histogram presentation of GO classification indicates transcripts in numbers after being annotated in three groups: CC, MF, and BP. E–G KEGG analysis of upregulation and downregulation of TOP20 in the transcriptome of embryonic knockdown Lr-pgrn-s1. The top enrichment pathways are presented in the advanced bubble chart. The X-axis label represents the enrichment score, while the Y-axis label represents the pathway. The size of the bubble represents the number of genes enriched in the KEGG terms, while the color represents the FDR P-value of KEGG terms. H qRT-PCR analysis of genes related to the MAPK, Notch, Wnt, and TGF-β signaling pathways. Mean ± SD is shown (n = 3 per group). The probability of statistical differences between the experimental groups was determined using Student’s t-test. *P < 0.05, **P < 0.001, ***P < 0.0001