Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process
Abstract
:1. Introduction
2. Methods
2.1. Identification and Analysis of DEGs
2.2. Integration Analysis of ATAC-Seq and RNA-Seq
2.3. Structure Analysis of Candidate GPCR Proteins
2.4. Artemia Hatching and Culture
2.5. Verification of Changes in Genes Expression for Candidate GPCRs
3. Results
3.1. DEG Analysis of Genes from ATAC-Seq
3.2. DEG Analysis of Genes from RNA-Seq
3.3. Integration Analysis of DEGs from ATAC-Seq and RNA-Seq
3.4. Structure Analysis of the Candidate GPCR Genes
3.5. Verification of Changes in Gene Expression for Candidate GPCRs
3.6. Comparison with Interim Results
4. Discussion
4.1. Signal Regulation of Embryonic Reactivation Process
4.2. Other Pathways Involved in Embryonic Reactivation
4.3. GPCRs Participating in Artemia Embryonic Reactivation Process
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
TMH | Trans-membrane helix |
DEGs | Differentially expressed genes |
GPCR | G-protein-coupled receptor |
TSS | Downstream gene start site |
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Subject | Up-Regulated | Down-Regulated | Total |
---|---|---|---|
ATAC-seq | 7124 | 5399 | 9159 |
RNA-seq | 3608 | 3251 | 6859 |
Integrated DEGs | 2005 | 1111 | 3116 |
Candidate GPCR Genes | Gene Name | TMHMM | PredictProtein | SWISS-MODEL |
---|---|---|---|---|
evm.TU.ctg485.29 | ADGRE5 | 7 | 7 | 7 |
evm.TU.ctg1078.1 | AR | 7 | 7 | 7 |
evm.TU.ctg530.1 | ADRB3 | 7 | 7 | 7 |
evm.TU.ctg71.25 | GRM5 | 7 | 7 | 7 |
evm.TU.ctg179.30 | UVOP | 6 | 7 | 7 |
evm.TU.ctg441.12 | RYa-R | 7 | 7 | 7 |
evm.TU.ctg428.23 | HRH1 | 7 | 7 | 7 |
evm.TU.ctg201.8 | Adgrl1 | 7 | 7 | 7 |
evm.TU.ctg54.13 | NPFR | 7 | 7 | 6 |
evm.TU.ctg310.11 | Gabbr1 | 7 | 6 | 7 × 2 |
evm.TU.ctg394.6 | Dop1R2 | 6 | 7 | 7 |
evm.TU.ctg3.36 | gar-2 | 6 | 6 | 5 |
evm.TU.ctg92.26 | CCAP-R | 5 | 6 | 5 |
evm.TU.ctg150.6 | stan | 5 | 6 | 0 |
evm.TU.ctg288.3 | Cirl | 5 | 5 | 5 |
evm.TU.ctg73.14 | QRFPR | 5 | 5 | 6 |
evm.TU.ctg640.11 | SCOP1 | 4 | 5 | 5 |
evm.TU.ctg195.9 | CCKAR | 4 | 4 | 5 |
evm.TU.ctg275.30 | TkR86C | 4 | 4 | 4 |
evm.TU.ctg889.7 | moody | 4 | 4 | 2 |
evm.TU.ctg116.37 | mth2 | 3 | 3 | 4 |
evm.TU.ctg155.21 | HRH1 | 3 | 3 | 3 |
evm.TU.ctg16.15 | 7tm_1 | 3 | 3 | 3 |
evm.TU.ctg397.21 | Svep1 | 2 | 1 | 0 |
evm.TU.ctg88.22 | mAChR-A | 1 | 1 | 1 |
evm.TU.ctg469.18 | NA | 1 | 1 | 0 |
evm.TU.ctg25.48 | Pep-like | 0 | 0 | 0 |
evm.TU.ctg212.15 | SCAF8 | 0 | 0 | 0 |
evm.TU.ctg115.32 | FKBP4 | 0 | 0 | 0 |
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Li, A.; Song, Z.; Zhang, M.; Duan, H.; Sui, L.; Wang, B.; Hao, T. Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process. Genes 2024, 15, 1083. https://doi.org/10.3390/genes15081083
Li A, Song Z, Zhang M, Duan H, Sui L, Wang B, Hao T. Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process. Genes. 2024; 15(8):1083. https://doi.org/10.3390/genes15081083
Chicago/Turabian StyleLi, Anqi, Zhentao Song, Mingzhi Zhang, Hu Duan, Liying Sui, Bin Wang, and Tong Hao. 2024. "Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process" Genes 15, no. 8: 1083. https://doi.org/10.3390/genes15081083