Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities
Abstract
:1. Introduction
2. Brief Overview of Single-Cell and Single-Nuclei mRNA and ATAC Sequencing
2.1. Cell Isolation, Library Preparation, and Sequencing
2.2. Bioinformatic Analyses
2.3. Data Interpretation
3. Current Uses of Single-Cell Sequencing in Ruminant Livestock Research
3.1. Cellular Heterogeneity within Tissues Important for Food and Fiber Production
3.2. Gene Expression Dynamics during Reproduction and Development at Single-Cell Resolution
3.3. Immune Cell Gene Expression and Chromatin Profiling
4. Challenges and Limitations of Single-Cell Technologies in Ruminant Livestock Research
4.1. Technical and Bioinformatic Challenges
4.2. Cell Cluster Identification and Spatial Resolution
4.3. Reproducibility, Collaboration, and Knowledge Sharing
5. The Future of Single-Cell Sequencing in Ruminant Livestock Research
6. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Tissue(s) or Cell Type(s) | Isolation Type | Data Type | Database and Accession * | Reference |
---|---|---|---|---|
Abomasum, ileum, liver, mammary gland, omasum, PBMC *, rectum, reticulum, rumen, salivary gland | Cell | RNA | GEO GSE176512 | [6] |
Adipose | Nuclei | RNA | GEO GSE211707 | [7] |
Embryo (8- and 16-cell stage) | Cell | RNA | GEO GSE99210 | [8] |
Embryo (peri-implantation) | Cell | RNA | GEO GSE234335 | [9] |
Embryo (SCNT) | Cell | RNA | SRA PRJNA727165 | [10] |
Embryo (trophectoderm) | Cell | RNA | GEO GSE200216 | [11] |
Fetal Gonads | Cell | RNA | GEO GSE162952 | [12] |
Milk Somatic Cells | Cell | RNA | ENA PRJEB73560 | [13] |
Muscle | Cell | RNA | GEO GSE205347 | [14] |
Muscle | Cell | RNA, ATAC | GSA CRA006626 | [15] |
PBMC * | Cell | RNA, ATAC | GEO GSE225962 | [16] |
PBMC * | Cell | RNA, ATAC | GEO GSE166473 | [17] |
Placenta (developing) | Cell | RNA | GEO GSE234524 | [18] |
Placenta (mature) | Nuclei | RNA | GEO GSE214407 | [19] |
Primary Mammary Epithelial Cells | Cell | RNA | FAANG PRJEB41576 | [20] |
Ruminal epithelial cells | Cell | RNA | GEO GSE166473 | [21] |
Satellite cells | Cell | RNA | GEO GSE184128 | [22] |
Satellite cells | Cell | RNA | GEO GSE211428 | [23] |
Tissue(s) or Cell Type(s) | Isolation Type | Data Type | Database and Accession * | Reference |
---|---|---|---|---|
Conceptus | Cell | RNA | NCBI PRJNA987334 | [24] |
Embryo | Cell | RNA | GEO GSE185233 | [25] |
Ovary | Cell | RNA | GEO GSE233801 | [26] |
Rumen | Cell | RNA | GSA CRA007511 | [27] |
Rumen | Cell | RNA | NCBI PRJNA919098 | [28] |
Skin | Cell | RNA | GEO GSE186204 | [29] |
Testes | Cell | RNA | GEO GSE184343 | [30] |
Testes | Cell | RNA | GSA CRA005236 | [31] |
Tissue(s) or Cell Type(s) | Isolation Type | Data Type | Database and Accession * | Reference |
---|---|---|---|---|
Fetal Gonad | Cell | RNA, ATAC | GSA CRA006304, CRA006365 | [32] |
Lung | Nuclei | RNA | GEO GSE183300 | [33] |
Ovarian Follicle | Cell | RNA | GEO GSE135688 | [34] |
Ovary | Cell | RNA | NCBI PRJNA1010653 | [35] |
Rumen | Cell | RNA | NCBI PRJNA919098 | [28] |
Skin | Cell | RNA | GEO GSE144351 | [36] |
Skin | Cell | RNA | GEO GSE182474 | [37] |
Skin | Cell | RNA | GEO GSE141284 | [38] |
Testes | Cell | RNA | GEO GSE234407 | [39] |
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Lyons, A.; Brown, J.; Davenport, K.M. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Curr. Issues Mol. Biol. 2024, 46, 5291-5306. https://doi.org/10.3390/cimb46060316
Lyons A, Brown J, Davenport KM. Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. Current Issues in Molecular Biology. 2024; 46(6):5291-5306. https://doi.org/10.3390/cimb46060316
Chicago/Turabian StyleLyons, Avery, Jocelynn Brown, and Kimberly M. Davenport. 2024. "Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities" Current Issues in Molecular Biology 46, no. 6: 5291-5306. https://doi.org/10.3390/cimb46060316