The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Open accessAbstract
The mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single cell RNA-seq. Zygotic genome activation correlates with the presence of polycomb repressive complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species, stage and lineage specific. The pluripotency network in the primate epiblast lacks certain regulators that are operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and non-human primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development, and underscores the molecular adaptability of early mammalian embryogenesis.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
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
Self-organized formation of topologically correct feature maps
Kohonen, T. (1982) · Biological Cybernetics · doi:10.1007/bf00337288 · Cited by 9,529
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143
A General Framework for Weighted Gene Co-Expression Network Analysis
Zhang, B., & Horvath, S. (2005) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1128 · Cited by 5,684
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · cited 2×
“Samples were stage matched to permit direct cross-species comparison, and sequencing libraries for all constituent samples were produced using the Smart-seq protocol (Picelli et al., 2013) to minimise technical differences.”
MethodSingle-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
Deng, Q., Ramsköld, D., Reinius, B., & Sandberg, R. (2014) · Science · doi:10.1126/science.1245316 · Cited by 1,345
Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo
Arnold, S. J., & Robertson, E. J. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2618 · Cited by 816 · cited 1×
“The amnion is specified via the amniochorionic fold during gastrulation (Arnold and Robertson, 2009; Rossant and Tam, 2009; Pereira et al., 2011).”
BackgroundThomas, P. Q., Brown, A., & Beddington, R. S. P. (1998) · Development · doi:10.1242/dev.125.1.85 · Cited by 528
Ohnishi, Y., Huber, W., Tsumura, A., Kang, M., Xenopoulos, P., Kurimoto, K., Oleś, A. K., Araúzo-Bravo, M. J., Saitou, M., Hadjantonakis, A.-K., et al. (2014) · Nature Cell Biology · doi:10.1038/ncb2881 · Cited by 300
Kang, M., Piliszek, A., Artus, J., & Hadjantonakis, A.-K. (2013) · Development · doi:10.1242/dev.084996 · Cited by 284
Strogantsev, R., Krueger, F., Yamazawa, K., Shi, H., Gould, P., Goldman-Roberts, M., McEwen, K., Sun, B., Pedersen, R., & Ferguson-Smith, A. C. (2015) · Genome Biology · doi:10.1186/s13059-015-0672-7 · Cited by 152
Cited by
Development of the human placenta
Turco, M. Y., & Moffett, A. (2019) · Development · doi:10.1242/dev.163428 · Cited by 698
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids
Liu, X., Tan, J. P., Schröder, J., Aberkane, A., Ouyang, J. F., Mohenska, M., Lim, S. M., Sun, Y. B. Y., Chen, J., Sun, G., et al. (2021) · Nature · doi:10.1038/s41586-021-03372-y · Cited by 361
The evolving concept of cell identity in the single cell era
Morris, S. A. (2019) · Development · doi:10.1242/dev.169748 · Cited by 154
Animal models of human pregnancy and placentation: alternatives to the mouse
Carter, A. M. (2020) · Reproduction · doi:10.1530/rep-20-0354 · Cited by 130
Taguchi, J., Shibata, H., Kabata, M., Kato, M., Fukuda, K., Tanaka, A., Ohta, S., Ukai, T., Mitsunaga, K., Yamada, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25249-4 · Cited by 46
Metadata
- Authors
- Boroviak, T., Stirparo, G. G., Dietmann, S., Hernando-Herraez, I., Mohammed, H., Reik, W., Smith, A., Sasaki, E., Nichols, J., & Bertone, P.
- Venue
- Development
- Publisher
- The Company of Biologists
- Published
- 2018-11-01
- Volume
- 145
- Issue
- 21
- ISSN
- 0950-1991 (ISSN-L)
- 1477-9129
- OpenAlex
- W2950703447
- Cited by
- 214
- References
- 18
- FWCI
- 6.83
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
