Comparative transcriptome profile analysis of granulosa cells from porcine ovarian follicles during early atresia

Figures & data

Figure 1. Gene distribution and expression profiles. (A) Length distribution of transcripts and unigenes. (B) Box plot showing overall RPKM expression values of each sample. (C) The RPKM density distribution of unigenes. (D) Principal component analysis (PCA) of the gene expression data (the principal components 1 and 2 accounted for 59.7 and 37.5 of variance).

Table 1. Summary of sequencing reads aligned with the Sus scrofa genome and mapped genes.

Sample	HF1	HF2	HF3	EAF1	EAF2	EAF3
Clean reads	110,971,804	103,220,112	118,990,004	89,128,644	113,109,952	88,269,906
rRNA reads	538,874	1,068,304	503,660	334,594	472,586	339,710
Effective reads	110,432,930	102,151,808	118,486,344	88,794,050	112,637,356	87,930,196
Effective reads/Clean reads	99.51%	98.97%	99.58%	99.62%	99.58%	99.62%
Total mapped	88,995,590	80,451,717	97,025,526	70,416,735	92,173,152	70,855,707
Total mapped/Effective reads	80.59%	78.76%	81.89%	79.3%	81.83%	80.58%
Uniquely mapped	14,116,903	11,498,381	80,927,353	59,332,060	77,643,716	59,769,179
Multiple mapped	74,878,687	68,953,336	16,098,173	11,084,675	14,529,436	11,086,528
Uniquely mapped/Total mapped	67.8%	67.5%	68.3%	66.82%	68.93%	67.97%
Exonic	58,481,098	48,016,013	69,278,698	42,918,261	63,224,505	44,113,134
Intergenic	12,360,815	12,923,834	11,481,449	12,052,757	11,659,063	11,977,229
Splicing	27,198	30,816	25,090	22,689	27,665	22,011
Intronic	18,126,479	19,481,054	16,240,289	15,423,028	17,261,919	14,743,333

HF: Healthy follicles; EAF: Early atretic follicles.

Figure 2. Volcano map and hierarchical clustering analysis showing the expression profiles between HF and EAF. (A) Volcano maps show the detected DEGs. Red dots represent the DEGs with corrected p < 0.05 and |log2(fold change)| ≥ 1, FDR < 0.05, and RPKM > 100. (B) The heatmap shows the hierarchical clustering of DEGs. Yellow represents the upregulated genes, and blue represents the downregulated ones.

Figure 3. GO enrichment analysis of DEGs. The No. of genes indicates the number of inputs of DEGs annotated to the category, and the X-axis represents − log10 (p value).

Figure 4. The pathway analysis of DEGs. (A) KEGG enrichment analysis of DGEs. The size of each dot represents the number of DEGs enriched in the corresponding pathway. (B) The ovarian steroidogenesis pathway with DEGs is highlighted in pink.

Figure 5. Protein–protein interaction network of DEGs. Lines of different colors represent seven types of evidence used in predicting associations. red: fusion evidence; green line: neighborhood evidence; blue: co-occurrence evidence; purple: experimental evidence; yellow: text mining evidence; light blue: database evidence; black: co-expression evidence.

Figure 6. qPCR validation of 11 DEGs between HF and EAF. The black columns represent the log₂RPKM value (left Y-axis) generated by RNA-seq, and the grey columns represent the qPCR fold changes (right Y-axis) and are expressed as means of three samples. **p < 0.01.