Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak
Abstract
:1. Introduction
2. Results
2.1. ATAC-Seq Quality Control of the White Yak Longissimus Dorsi Muscle
2.2. Chromatin Accessibility in the Longissimus Dorsi Muscle of the White Yak
2.3. RNA-Seq Data from Longissimus Dorsi Muscle of the White Yak
2.4. Combined Analysis of ATAC-Seq and RNA-Seq
2.5. Validation of the Results by RT-qPCR
3. Discussion
4. Materials and Methods
4.1. Collection of Samples
4.2. ATAC-Seq
4.3. RNA-Seq
4.4. Integration Analysis of ATAC-Seq and RNA-Seq
4.5. Gene Functional Annotation
4.6. RT-qPCR
4.7. Statistical Analysis
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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Sample | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Clean Ratio | Q20 | Q30 |
---|---|---|---|---|---|---|---|
A_1 | 128,541,756 | 19,281,263,400 | 127,569,914 | 13,604,132,565 | 99.24% | 98.36% | 95.01% |
A_2 | 89,333,144 | 13,399,971,600 | 88,641,850 | 11,625,646,313 | 99.23% | 98.76% | 95.87% |
C_1 | 135,034,832 | 20,255,224,800 | 133,887,694 | 17,651,791,047 | 99.15% | 98.63% | 95.46% |
C_2 | 77,318,490 | 11,597,773,500 | 77,040,194 | 9,515,338,581 | 99.64% | 99.00% | 96.47% |
Sample | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Clean Ratio | Q20 | Q30 |
---|---|---|---|---|---|---|---|
A_1 | 78,265,742 | 11,739,861,300 | 77,683,168 | 11,626,880,356 | 99.26% | 98.25% | 94.88% |
A_2 | 53,208,116 | 7,981,217,400 | 52,829,996 | 7,906,568,770 | 99.29% | 98.24% | 94.80% |
A_3 | 121,439,410 | 18,215,911,500 | 120,564,720 | 18,063,425,239 | 99.28% | 98.23% | 94.76% |
C_1 | 102,222,314 | 15,333,347,100 | 101,316,102 | 15,149,604,968 | 99.11% | 98.10% | 94.56% |
C_2 | 36,264,690 | 5,439,703,500 | 35,877,070 | 5,370,251,031 | 98.93% | 98.19% | 94.77% |
C_3 | 101,895,462 | 15,284,319,300 | 101,061,120 | 15,133,341,000 | 99.18% | 98.17% | 94.70% |
Primer | Sequence (5′–3′) | Product Size |
---|---|---|
ANKRD2-F | CCTGAGAGTCCGTCCTTAC | 141 bp |
ANKRD2-R | CCGTTTCTTCTGCTTGCGT | |
PLEKHA4-F | GGCAATGCTCTCAGAAGGGA | 118 bp |
PLEKHA4-R | AATGGCCAGAGAGGACGAAC | |
ZNF503-F | CGCTCTCTGGAAATAGCTCCG | 122 bp |
ZNF503-R | CTTGATGGGCAGGCGGTTAG | |
ANKRD1-F | AGAAGAAAGGCAGTGGGGATG | 121 bp |
ANKRD1-R | ACAAAGTGGACCGGAAGTGT | |
BTG2-F | GCATCCGCATCAACCACAAG | 217 bp |
BTG2-R | TTCTTGCAGGTGAGAAGCCC | |
FOS-F | TACAGCCCACCCTAGTCTCC | 71 bp |
FOS-R | AGTAGGGACTCCATAGGGGTG | |
FOXO1-F | ACCCCACAAGGTTTCCGATG | 90 bp |
FOXO1-R | AGTGTCCCCTCTCTTTCCAAC | |
LMOD3-F | CCACCTTGTCCCCAGAAGAG | 129 bp |
LMOD3-R | GGTCGAAGTTCCCTGTTGGT | |
UCP3-F | CGGACCACTCCAGCATCATT | 186 bp |
UCP3-R | CTTCCTCTCTGGCGATGGTC | |
GAPDH-F | CCACGAGAAGTATAACAACACC | 120 bp |
GAPDH-R | GTCATAAGTCCCTCCACGAT |
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Li, J.; Chen, Z.; Bai, Y.; Wei, Y.; Guo, D.; Liu, Z.; Niu, Y.; Shi, B.; Zhang, X.; Cai, Y.; et al. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int. J. Mol. Sci. 2024, 25, 158. https://doi.org/10.3390/ijms25010158
Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, et al. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. International Journal of Molecular Sciences. 2024; 25(1):158. https://doi.org/10.3390/ijms25010158
Chicago/Turabian StyleLi, Jingsheng, Zongchang Chen, Yanbin Bai, Yali Wei, Dashan Guo, Zhanxin Liu, Yanmei Niu, Bingang Shi, Xiaolan Zhang, Yuan Cai, and et al. 2024. "Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak" International Journal of Molecular Sciences 25, no. 1: 158. https://doi.org/10.3390/ijms25010158