Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animal and Sample Preparation
2.3. Total RNA and Protein Isolation from Lung Samples
2.4. Library Preparation and RNA Sequencing
2.5. Differential Gene Analysis Using RNA-seq
2.6. Proteolysis and Labelling
2.7. Database Search, Protein Identification, and Quantification
2.8. RT-qPCR of Candidate Genes
3. Results
3.1. Summary of RNA-seq Data
3.2. Functional Annotation of DEGs
3.3. RNA-seq Date Validation by RT-qPCR
3.4. Protein Identification and Quantification
3.5. Functional Annotation of DEPs
3.6. Combined Analysis of DEGs in RNA-seq and DEPs in iTRAQ
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | Gene Name | Log2 Fold Change | p-Value | Up/Down |
---|---|---|---|---|
ENSSSCG00000009738 | GALNT9 | 7.689227 | 1.83 × 10−6 | up |
ENSSSCG00000033254 | IFN-ALPHA-13 | 6.983059 | 1.02 × 10−6 | |
ENSSSCG00000007859 | UMOD | 6.040727 | 0.009784 | |
ENSSSCG00000033610 | ZG16B | 6.015486 | 0.024330 | |
ENSSSCG00000037533 | HIST2H2AB | 5.656798 | 0.001126 | |
ENSSSCG00000029516 | SLC22A8 | 5.639100 | 0.020157 | |
ENSSSCG00000034995 | RF00017 | 5.098178 | 0.035442 | |
ENSSSCG00000037202 | CACNG4 | 4.860514 | 0.013594 | |
ENSSSCG00000037225 | RPRM | 4.856914 | 0.016825 | |
ENSSSCG00000008741 | FGFBP1 | 4.832671 | 0.000081 | |
ENSSSCG00000037535 | SLC34A1 | 4.729766 | 0.013466 | |
ENSSSCG00000037300 | GRP | 4.443211 | 0.005612 | |
ENSSSCG00000035689 | NEXMIF | 4.430799 | 0.043955 | |
ENSSSCG00000001906 | CYP1A1 | 4.426375 | 0.000505 | |
ENSSSCG00000003066 | IRGC | 4.404553 | 0.047451 | |
ENSSSCG00000033193 | TPO | 4.400171 | 0.016735 | |
ENSSSCG00000037534 | OPCML | 4.233214 | 4.60 × 10−16 | |
ENSSSCG00000001613 | TREML1 | 4.174212 | 0.003859 | |
ENSSSCG00000028695 | TMSB15A | 4.032314 | 3.94 × 10−14 | |
ENSSSCG00000022140 | TMPRSS11E | 4.005328 | 0.028356 | |
ENSSSCG00000040910 | APOH | −4.214353 | 0.027279 | down |
ENSSSCG00000021767 | TDH | −4.268103 | 0.001937 | |
ENSSSCG00000002479 | SERPINA11 | −4.286988 | 0.006838 | |
ENSSSCG00000012711 | F9 | −4.323437 | 0.026465 | |
ENSSSCG00000016159 | CPS1 | −4.326881 | 0.000381 | |
ENSSSCG00000012517 | TMSB15B | −4.341481 | 5.88 × 10−7 | |
ENSSSCG00000016856 | C9 | −4.466406 | 0.037223 | |
ENSSSCG00000010431 | A1CF | −4.487968 | 0.017588 | |
ENSSSCG00000003835 | C8A | −4.594111 | 0.000224 | |
ENSSSCG00000020680 | CLDN14 | −4.631278 | 0.006969 | |
ENSSSCG00000008998 | FGA | −4.729940 | 0.002310 | |
ENSSSCG00000036158 | TRAM1L1 | −4.734145 | 0.003310 | |
ENSSSCG00000037547 | SLC17A3 | −4.893193 | 0.000000 | |
ENSSSCG00000006248 | MOS | −5.303923 | 0.006916 | |
ENSSSCG00000002983 | LGALS13 | −5.369302 | 0.000084 | |
ENSSSCG00000034429 | PLA2G5 | −5.410249 | 0.010311 | |
ENSSSCG00000029449 | PRG4 | −5.667579 | 4.54 × 10−20 | |
ENSSSCG00000016315 | SPP2 | −6.047557 | 0.000038 | |
ENSSSCG00000008214 | FABP1 | −6.452786 | 0.000014 | |
ENSSSCG00000037268 | APCS | −7.280566 | 2.05 × 10−7 |
Accession | Gene Name | MW [kDa] | FC | p-Value | Log2FC | |
---|---|---|---|---|---|---|
A0A286ZWS8 | COL2A1 | 141.6 | 4.119454 | 0.321115 | 2.042453 | up |
F8WSC1 | SLA-1 | 40 | 3.918033 | 0.357562 | 1.970129 | |
V9PR54 | SLA-1 | 40.4 | 3.158697 | 0.138104 | 1.659330 | |
A0A287AEL2 | KRT14 | 56 | 3.135079 | 0.288655 | 1.648502 | |
A0A287ATD0 | KRT75 | 58.7 | 3.059540 | 0.166403 | 1.613315 | |
I3L8B2 | COL9A2 | 65.1 | 2.900520 | 0.371928 | 1.536312 | |
A0A287B863 | ACAN | 251.9 | 2.875969 | 0.352952 | 1.524048 | |
F1S571 | COL11A1 | 147.1 | 2.861647 | 0.081541 | 1.516846 | |
F1REZ1 | HAPLN1 | 40.2 | 2.843049 | 0.359189 | 1.507439 | |
A0A286ZI25 | PARP14 | 200.9 | 2.780718 | 0.354096 | 1.475458 | |
F2Z501 | TMED2 | 21.7 | 2.649027 | 0.073811 | 1.405462 | |
F1S0J1 | C4BPA | 22.7 | 2.597122 | 0.012400 | 1.376914 | |
F1SCU3 | MATN3 | 52.7 | 2.556017 | 0.376462 | 1.353897 | |
F1RXG1 | KRT27 | 49.7 | 2.384095 | 0.227473 | 1.253442 | |
A5A758 | KRT1 | 65.2 | 2.333889 | 0.126611 | 1.222736 | |
A0A287A461 | CHAD | 40.6 | 2.294893 | 0.355746 | 1.198427 | |
F1S7K4 | PLIN4 | 158.7 | 2.237992 | 0.010325 | 1.162205 | |
I3LDS3 | KRT10 | 58.9 | 2.234501 | 0.340817 | 1.159953 | |
I3L5Q7 | MATN1 | 53.9 | 2.227542 | 0.361420 | 1.155452 | |
A7J149 | BPIFB1 | 51.9 | 2.227004 | 0.377700 | 1.155104 | |
F1SIT7 | RPLP1 | 11.5 | 0.576307 | 0.013941 | −0.795091 | down |
F1RW28 | HSD17B13 | 33.3 | 0.561833 | 0.013894 | −0.831787 | |
F1RL41 | UPB1 | 42.9 | 0.560874 | 0.035026 | −0.834251 | |
A0A287BN06 | PZP | 158.1 | 0.560354 | 0.006529 | −0.835590 | |
B5L2L8 | SLA-DQA | 9.5 | 0.546931 | 0.058481 | −0.870568 | |
A0A0A7BZH1 | SLA-DQB1 | 29.5 | 0.538462 | 0.365487 | −0.893085 | |
L7UWL8 | SLA-2 | 20.7 | 0.538067 | 0.396005 | −0.894142 | |
A0A2C9F382 | FABP1 | 16.5 | 0.537673 | 0.051562 | −0.895199 | |
A0A2C9F343 | LYZ | 16.5 | 0.508926 | 0.014242 | −0.974471 | |
Q8HX61 | SLA-B | 40.6 | 0.482827 | 0.230141 | −1.050422 | |
B6DU23 | SLA-DRB1 | 10.8 | 0.470833 | 0.319788 | −1.086712 | |
B6ICW6 | SLA-2 | 40.5 | 0.445435 | 0.385493 | −1.166714 | |
D3GIN8 | SLA-2 | 38.8 | 0.435303 | 0.022197 | −1.199910 | |
K9J6H8 | A2M | 163.9 | 0.430956 | 0.069842 | −1.214386 | |
A0A1L1YNR3 | FASN | 93.4 | 0.423150 | 0.060034 | −1.240759 | |
T2HGI4 | SLA-1 | 35 | 0.404494 | 0.333977 | −1.305808 | |
D3GIP1 | SLA-3 | 40.4 | 0.402103 | 0.005976 | −1.314364 | |
I3LLB7 | PIK3R1 | 83.5 | 0.396648 | 0.039119 | −1.334069 | |
F1SER3 | SFTPA1 | 26.5 | 0.389442 | 0.017424 | −1.360520 | |
A0A1C9J6L2 | SLA-1 | 40.1 | 0.231828 | 0.016153 | −2.108876 |
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Shang, P.; Zhang, B.; Li, P.; Ahmed, Z.; Hu, X.; Chamba, Y.; Zhang, H. Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs. Animals 2022, 12, 1919. https://doi.org/10.3390/ani12151919
Shang P, Zhang B, Li P, Ahmed Z, Hu X, Chamba Y, Zhang H. Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs. Animals. 2022; 12(15):1919. https://doi.org/10.3390/ani12151919
Chicago/Turabian StyleShang, Peng, Bo Zhang, Pan Li, Zulfiqar Ahmed, Xiaoxiang Hu, Yangzom Chamba, and Hao Zhang. 2022. "Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs" Animals 12, no. 15: 1919. https://doi.org/10.3390/ani12151919
APA StyleShang, P., Zhang, B., Li, P., Ahmed, Z., Hu, X., Chamba, Y., & Zhang, H. (2022). Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs. Animals, 12(15), 1919. https://doi.org/10.3390/ani12151919