Spatio-temporal mRNA tracking in the early zebrafish embryo(Dataset ID: STDS0000076)
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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
Contributors
Karoline Holler; Anika Neuschulz; Philipp Boß; Janita Mintcheva; Roberto Arsiè; Uwe Ohler; Markus Landthaler; Jan P Junker
Contact: JanPhilipp.Junker@mdc-berlin.de
Accessions
GEO Series Accessions:
GSE158849
Reference way
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