The DOI matches its Crossref record; 101 of the 101 references it cites were found in a registry or an index.
A high-resolution mRNA expression time course of embryonic development in zebrafish
Open accessAbstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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R: A Language and Environment for Statistical Computing
R Core Team (2025) · doi:10.32614/r.manuals · Cited by 352,181
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
Salmon provides fast and bias-aware quantification of transcript expression
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,116
Stages of embryonic development of the zebrafish
Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B., & Schilling, T. F. (1995) · Developmental Dynamics · doi:10.1002/aja.1002030302 · Cited by 12,037
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148
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Vastenhouw, N. L., Cao, W. X., & Lipshitz, H. D. (2019) · Development · doi:10.1242/dev.161471 · Cited by 445
Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome
Calixto, C. P. G., Guo, W., James, A. B., Tzioutziou, N. A., Entizne, J. C., Panter, P. E., Knight, H., Nimmo, H. G., Zhang, R., & Brown, J. W. S. (2018) · The Plant Cell · doi:10.1105/tpc.18.00177 · Cited by 298
Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101
The gene regulatory basis of genetic compensation during neural crest induction
Dooley, C. M., Wali, N., Sealy, I. M., White, R. J., Stemple, D. L., Collins, J. E., & Busch-Nentwich, E. M. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008213 · Cited by 40
Self-citationGag proteins encoded by endogenous retroviruses are required for zebrafish development
Chang, N.-C., Wells, J. N., Wang, A. Y., Schofield, P., Huang, Y.-C., Truong, V. H., Simoes-Costa, M., & Feschotte, C. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2411446122 · Cited by 27
Metadata
- Authors
- White, R. J., Collins, J. E., Sealy, I. M., Wali, N., Dooley, C. M., Digby, Z., Stemple, D. L., Murphy, D. N., Billis, K., Hourlier, T., Füllgrabe, A., Davis, M. P., Enright, A. J., & Busch-Nentwich, E. M.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2017-11-16
- Volume
- 6
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2594035655
- Cited by
- 361
- References
- 101
- FWCI
- 8.74
- Type
- journal article
- Language
- en
- Open access
- gold
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- White, R. J., Collins, J. E., Sealy, I. M., Wali, N., Dooley, C. M., Digby, Z., Stemple, D. L., Murphy, D. N., Billis, K., Hourlier, T., Füllgrabe, A., Davis, M. P., Enright, A. J., & Busch-Nentwich, E. M. (2017). A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife. https://doi.org/10.7554/elife.30860
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