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| Status |
Public on Dec 07, 2020 |
| Title |
Spatio-temporal mRNA tracking in the early zebrafish embryo |
| Organisms |
Danio rerio; Xenopus laevis; Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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.
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| 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.
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/34099733/
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| |
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| Contributor(s) |
Holler K, Neuschulz A, Boß P, Mintcheva J, Arsiè R, Ohler U, Landthaler M, Junker JP |
| Citation(s) |
34099733 |
| |
| Submission date |
Sep 30, 2020 |
| Last update date |
Jul 15, 2021 |
| Contact name |
Jan Philipp Junker |
| E-mail(s) |
JanPhilipp.Junker@mdc-berlin.de
|
| Organization name |
MDC
|
| Department |
BIMSB
|
| Lab |
Junker
|
| Street address |
Hannoversche Str. 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
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| Platforms (4)
|
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
| GPL21248 |
Illumina NextSeq 500 (Xenopus laevis) |
| GPL21741 |
Illumina HiSeq 4000 (Danio rerio) |
| GPL24884 |
Illumina NextSeq 500 (Xenopus tropicalis) |
|
| Samples (8)
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| Relations |
| BioProject |
PRJNA666689 |
| SRA |
SRP285948 |
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