Spatio-temporal mRNA tracking in the early zebrafish embryo(Dataset ID: STDS0000076)

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Genes: 32,250
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PMID: 34099733
Summary
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Dataset information
Summary:
We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.
Overall design:
Spatial transcriptomic data (tomo-seq) from zebrafish one-cell stage embroys, mature X. laevis and X. tropicalis oocytes. Single-cell metabolic labeling (scSLAM-seq) of zebrafish embryos at 6 hpf.
Technology:
Tomo-seq
Platform:
GPL20828, GPL21248, GPL21741, GPL24884
Species:
Danio rerio(danRer10)
Xenopus laevis(XENLA_9.2)
Xenopus tropicalis(xenTro9)
Tissues:
Embryo
Organ parts:
Embryo
Submission date: 2020-09-30Update date: 2021-07-15
DOI: To be continue
Contributors
Karoline Holler,Anika Neuschulz,Philipp Boß,Janita Mintcheva,Roberto Arsiè,Uwe Ohler,Markus Landthal
Contact: JanPhilipp.Junker@mdc-berlin.de
Accessions
GEO Series Accessions: GSE158849
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Karoline Holler,Anika Neuschulz,Philipp Boß,Janita Mintcheva,Roberto Arsiè,Uwe Ohler,Markus Landthal. Spatio-temporal mRNA tracking in the early zebrafish embryo[DS/OL]. STOmicsDB, 2020[2020-09-30]. https://db.cngb.org/stomics/datasets/STDS0000076/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Holler, Karoline et al. “Spatio-temporal mRNA tracking in the early zebrafish embryo.” Nature communications vol. 12,1 3358. 7 Jun. 2021, doi:10.1038/s41467-021-23834-1