Deciphering the miRNA transcriptome of granulosa cells from dominant and subordinate follicles at first follicular wave in goat

Figures & data

Table 1. The specific primers used for qPCR.

miRNAs	Primer sequences (5′ → 3′)	miRNA sequences
chi-miR-107-3p	F: ACACTCCAGCTGGGAGCAGCATTGTACAG	AGCAGCAUUGUACAGGGCUAU
chi-miR-125a-3p	F: ACACTCCAGCTGGGACAGGTGAGGTTCTT	ACAGGUGAGGUUCUUGGGAGC
chi-miR-342-5p	F: ACACTCCAGCTGGGAGGGGTGCTATCTGTGG	AGGGGUGCUAUCUGUGGUUGAGG
chi-miR-129-3p	F: ACACTCCAGCTGGGAAGCCCTTACCCCAAA	AAGCCCUUACCCCAAAAAGCAU
chi-miR-331-3p	F: ACACTCCAGCTGGGCCCCTGGGCCTATCC	CCCCUGGGCCUAUCCUAGAAC
chi-miR-1343	F: ACACTCCAGCTGGGCTCCTGGGGCCCGCAC	CUCCUGGGGCCCGCACUCUCGC
chi-miR-874-3p	F: ACACTCCAGCTGGGCTGCCCTGGCCCGAGGG	CUGCCCUGGCCCGAGGGACCGAC
chi-miR-93-3p	F: ACACTCCAGCTGGGACTGCTGAGCCAGCACT	ACUGCUGAGCCAGCACUUCCCGA
novel_296	F: ACACTCCAGCTGGGTGCCAAGCCCACGTT	UGCCAAGCCCACGUUCAAAGG

Table 2. Quality control of small RNA sequencing data.

Sample	Raw reads	Clean reads	Clean reads/raw reads	Error rate	Q20	Q30	GC content
DF1	12,622,676	12,504,252	99.06%	0.01%	99.70%	99.10%	49.14%
DF2	15,556,673	15,216,187	97.81%	0.01%	99.67%	99.00%	49.62%
DF3	18,825,482	18,571,779	98.65%	0.01%	99.63%	98.90%	49.15%
SF1	14,227,266	13,980,174	98.26%	0.01%	99.60%	98.82%	49.33%
SF2	15,594,356	15,383,912	98.65%	0.01%	99.63%	98.87%	49.27%
SF3	16,478,036	16,363,269	99.30%	0.01%	99.65%	98.95%	49.20%

Figure 1. Length distribution of small RNAs in DF (A) and SF (B) granulosa cells.

Figure 2. Annotation classification of small RNAs in DF (A) and SF (B) granulosa cells.

Figure 3. Volcano map and hierarchical clustering analysis showing the expression profiles of miRNAs in DF and SF granulosa cells. (A) Volcano map shows the miRNAs expression with corrected P < 0.05 and |log2(fold change)| ≥ 1. Red dots represent the upregulated miRNAs, while blue dots represent the downregulated miRNAs. (B) The heatmap shows the significantly expressed miRNAs with corrected P < 0.05 and |log2(fold change)| ≥ 1.

Figure 4. GO enrichment analysis of target genes of differentially expressed miRNAs. Gene count indicates the number of inputs of target genes of differentially expressed miRNAs annotated to the category.

Figure 5. KEGG enrichment analysis of target genes of differentially expressed miRNAs. The size of each dot represents the number of target genes of differentially expressed miRNAs enriched in the corresponding pathway. A pathway with a corrected P value <0.05 is significantly overrepresented.

Figure 6. Potentially functional miRNAs and their predicted targeted genes compose this interactive network. The red triangle and green circles represent miRNAs and their targeted genes, respectively. The straight lines indicate the interaction.

Figure 7. Relative expression of follicular development-related miRNAs in DF and SF granulosa cells of goats. Data is presented as the mean ± SEM (n = 3), * and ** indicate significant differences P < 0.05 and P < 0.01, respectively.

Data availability statement

All datasets used in this study are available from the corresponding author on reasonable request.