2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Porcine Ovarian Granulosa Cells (pGCs) Culture In Vitro and under 2,5-HD Treatment
2.2. Cell Morphological Observations
2.3. Cell Apoptosis Detection
2.4. Phalloidin Staining
2.5. EDU Staining
2.6. Total RNA Extraction, Library Construction, and Sequencing Analysis
2.7. Quantitative PCR
2.8. CDKN1A Interference
2.9. Statistical Analysis
3. Results
3.1. Effect of 2,5-HD on pGC Morphology
3.2. Effect of 2,5-HD on Apoptosis of pGCs
3.3. Effect of 2,5-HD on pGC Proliferation
3.4. Gene Expression Profiling
3.5. Analysis of DEGs
3.6. KEGG and GO Analysis
3.7. Effect of CDKN1A on Apoptosis of pGCs
3.8. Effect of CDKN1A on the Cycle of pGCs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Production Number | Sample | Concentration-ng/uL | Volume/uL | Total/μg | RIN Value | Library Type | Conclusion |
---|---|---|---|---|---|---|---|
R18081118 | HD0-1 | 498 | 41 | 20.42 | 9.3 | RNA-seq | A |
R18081119 | HD0-2 | 465 | 41 | 19.07 | 10.0 | RNA-seq | A |
R18081120 | HD0-3 | 412 | 42 | 17.30 | 9.4 | RNA-seq | A |
R18081121 | HD40-1 | 308 | 40 | 12.32 | 9.5 | RNA-seq | A |
R18081122 | HD40-2 | 282 | 38 | 10.72 | 9.2 | RNA-seq | A |
R18081123 | HD40-3 | 225 | 40 | 9.00 | 9.7 | RNA-seq | A |
Gene Symbol | Primer Sequence (5′-3′) | Up/Down |
---|---|---|
MYH11 | GCGTCCATGCCAGATAACAC | Down |
CGCCCGACTTTGATACGTG | ||
MYCL | GGACCCCTGCATGAAACACT | Down |
CTGCCTCCTCTTCCTTTTCG | ||
RENBP | GAGTGGGCCATGAAGCTCT | Down |
CGAAACTGGCGAAACGTGTA | ||
DKK2 | TTTGCTGTGCACGTCACTTC | Down |
TTCTTGCGCTGCTTGGTACA | ||
F3 | ACGCCCTACCTGGACACAAA | Down |
TGCCGTTCACCCTGACTAAG | ||
BCLAF1 | GATTCGGAAGGGGATGACAC | Down |
CCTCCTCAGTATTCCGGTGA | ||
MDM2 | ACGACAAAGAAAGCGCCACA | Up |
ACTCACACCAGCGTCGAGAT | ||
CASP3 | CGGACAGTGGGACTGAAGAT | Up |
CGCCAGGAATAGTAACCAGG | ||
CDKN1A | GACCATGTGGACCTGTTGCT | Up |
GGCGTTTGGAGTGGTAGAAA | ||
SPP1 | AGAGACCCTGCCAAGCAAGT | Up |
ATGAGACTCGTCGGATCGGT | ||
SLC7A11 | TATCTCTGGCATTTGGACGC | Up |
GCACTCCAGCTGACACTCA | ||
IRAK2 | GCTCAGGTCCAGGATTGATTG | Up |
GCCCAGCAGAGGTAAGATGTT | ||
GAPDH | ATTCCACCCACGGCAAGTT | GAPDH-F |
TTTGATGTTGGCGGGATCT | GAPDH-R |
Gene | Target Sequence |
---|---|
si-ssc-CDKN1A_001 | CCAGCATGACAGATTTCTA |
si-ssc-CDKN1A_002 | CCAAACGCCGGCTGATCTT |
si-ssc-CDKN1A_003 | GCCGGCTGATCTTCTCCAA |
Sample | Before Filter | After Filter | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Clean | Q20 (%) | Q30 (%) | N (%) | GC (%) | HQ Clean | Q20 (%) | Q30 (%) | N (%) | GC (%) | |
Data (bp) | Data (bp) | |||||||||
HD0-1 | 8,546,605,500 | 8,344,655,111 (97.64%) | 8,047,846,082 (94.16%) | 1,288,743 (0.02%) | 4,550,166,659 (53.24%) | 8,224,210,048 | 8,107,811,882 (98.58%) | 7,867,744,147 (95.67%) | 857,487 (0.01%) | 4,374,980,230 (53.20%) |
HD0-2 | 10,701,057,900 | 10,470,640,137 (97.85%) | 10,123,251,944 (94.60%) | 1,615,274 (0.02%) | 5,683,390,145 (53.11%) | 10,322,343,616 | 10,187,549,091 (98.69%) | 9,903,589,358 (95.94%) | 1,073,648 (0.01%) | 5,478,669,969 (53.08%) |
HD0-3 | 9,492,620,100 | 9,284,411,677 (97.81%) | 8,972,299,225 (94.52%) | 1,432,089 (0.02%) | 5,053,549,739 (53.24%) | 9,147,813,875 | 9,026,488,425 (98.67%) | 8,771,971,839 (95.89%) | 949,030 (0.01%) | 4,866,908,860 (53.20%) |
HD40-1 | 8,278,856,700 | 809,754,7348 (97.81%) | 7,826,959,983 (94.54%) | 1,251,797 (0.02%) | 4,324,792,272 (52.24%) | 7,978,267,014 | 7,872,909,409 (98.68%) | 7,652,604,412 (95.92%) | 830,497 (0.01%) | 4,163,722,726 (52.19%) |
HD40-2 | 11,571,998,400 | 11,316,248,473 (97.79%) | 10,935,522,921 (94.50%) | 1,738,051 (0.02%) | 6,103,038,102 (52.74%) | 11,151,334,819 | 11,003,287,936 (98.67%) | 10,693,484,565 (95.89%) | 1,160,264 (0.01%) | 5,875,747,248 (52.69%) |
HD40-3 | 8,262,103,500 | 8,082,046,730 (97.82%) | 7,811,943,104 (94.55%) | 1,245,894 (0.02%) | 4,320,317,791 (52.29%) | 7,967,279,552 | 7,862,124,495 (98.68%) | 7,641,947,568 (95.92%) | 830,065 (0.01%) | 4,162,633,359 (52.25%) |
Gene ID | Gene Name | Control | 2,5-HD | Log2 Fold Change | Up/Down |
---|---|---|---|---|---|
ENSSSCG00000007554 | ZFAND2A | 411.333 | 8812.667 | 4.457916894 | Up |
ENSSSCG00000023298 | SRXN1 | 1613.667 | 24,429.000 | 4.006772443 | Up |
ENSSSCG00000008988 | CCNG2 | 411.667 | 4900.333 | 3.610374422 | Up |
ENSSSCG00000001488 | GCLC | 1608.333 | 17,005.667 | 3.483567018 | Up |
ENSSSCG00000022649 | SLC7A11 | 602.000 | 5672.333 | 3.33201828 | Up |
ENSSSCG00000010461 | ANKRD1 | 15,720.333 | 299.333 | 4.606115928 | Down |
ENSSSCG00000033657 | GREM1 | 6506.000 | 358.000 | 4.085838065 | Down |
ENSSSCG00000039514 | ID3 | 11,693.000 | 722.333 | 3.919259823 | Down |
ENSSSCG00000017723 | CCL2 | 16,245.333 | 1019.000 | 3.912958487 | Down |
ENSSSCG00000000146 | MYH11 | 24,112.870 | 1581.530 | 3.875688189 | Down |
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Chen, Y.; Kong, C.; Yang, M.; Liu, Y.; Han, Z.; Xu, L.; Zheng, X.; Ding, Y.; Yin, Z.; Zhang, X. 2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis. Vet. Sci. 2023, 10, 201. https://doi.org/10.3390/vetsci10030201
Chen Y, Kong C, Yang M, Liu Y, Han Z, Xu L, Zheng X, Ding Y, Yin Z, Zhang X. 2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis. Veterinary Sciences. 2023; 10(3):201. https://doi.org/10.3390/vetsci10030201
Chicago/Turabian StyleChen, Yige, Chengcheng Kong, Min Yang, Yangguang Liu, Zheng Han, Liming Xu, Xianrui Zheng, Yueyun Ding, Zongjun Yin, and Xiaodong Zhang. 2023. "2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis" Veterinary Sciences 10, no. 3: 201. https://doi.org/10.3390/vetsci10030201
APA StyleChen, Y., Kong, C., Yang, M., Liu, Y., Han, Z., Xu, L., Zheng, X., Ding, Y., Yin, Z., & Zhang, X. (2023). 2,5-Hexanedione Affects Ovarian Granulosa Cells in Swine by Regulating the CDKN1A Gene: A Transcriptome Analysis. Veterinary Sciences, 10(3), 201. https://doi.org/10.3390/vetsci10030201