GEO DataSets

(Submitter supplied) During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20828 GPL18413

446 Samples

Download data: MTX, TSV

(Submitter supplied) Wild-type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

2 Samples

Download data: MTX, TSV

(Submitter supplied) Wild-type zebrafish embryos were mechanically dissociated and profiled using Drop-seq

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

28 Samples

Download data: TXT

(Submitter supplied) SMART-seq2 was performed on single cells isolated from visually staged zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

416 Samples

Download data: TXT

(Submitter supplied) Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

9 Samples

Download data: TXT

(Submitter supplied) Study of transcriptome dynamics using a high-resolution gene-expression time course with 180 individual embryos, obtained from nine different spawns that are profiled from late blastula to mid gastrula stage. All individual embryos of genotype ABTL were photographed and an initial developmental time was estimated using percentage epiboly as a metric.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL22016

180 Samples

Download data: FTR, TXT

(Submitter supplied) Post-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

114 Samples

Download data: TSV, TXT

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL9998

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

21 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 ATG morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG) or Standard control morpholino (StCo). RNA was extracted at 12, 18 and 27hpf from both sets of embryos and compared with a two-colour hybridisation.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

9 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control). RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 mutant zebrafish in comparison to their sibling embryos. Embryos resulting from a cross between heterozygous hdac1 mutant zebrafish (hi1618/+) where cultured together then mutants separated from the siblings one the basis of phenotype and RNA extracted from the two groups at 27hpf was compared in a two-colour hybridisation.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

8 Samples

Download data: TXT

(Submitter supplied) Zebrafish is a popular model for studies of embryonic development. Recent surveys of zebrafish embryogenesis with single-cell transcriptomics have uncovered hundreds of cell types, but the dynamic accessible regions of the genome that determine regulatory programs responsible for the unique identity and function of each cell type during embryogenesis lack detailed study. Here, we present SPATAC-seq: a split-pool ligation-based high-throughput single-cell assay for transposase-accessible chromatin using sequencing. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30277 GPL30560 GPL24995

535 Samples

Download data: BED, BW, XLSX

(Submitter supplied) To establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25526 GPL26363

8 Samples

Download data: CSV, TSV

(Submitter supplied) 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. more...

Organism:

Danio rerio; Xenopus laevis; Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Here we performed single-cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified, spanning all three embryonic germ layers.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

1 Sample

Download data: MTX, TSV

(Submitter supplied) Heterochromatin has important functions in the organization of nuclear structure, the maintenance of genome integrity, and the regulation of gene expression programs1-3. Here, we demonstrate that the genome of the early zebrafish embryo is packaged in an atypical chromatin state that lacks features characteristic of heterochromatin. The heterochromatic histone modification, histone H3 lysine 9 trimethyl (H3K9me3), is undetectable in embryonic chromatin and embryonic nuclei are devoid of condensed chromatin prior to activation of the zygotic genome. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

20 Samples

Download data: TDF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by array

Platforms:

GPL14664 GPL7302

83 Samples

Download data

(Submitter supplied) Morpholino injections were performed to investigate transcriptional targets of Klf4, FoxD3 and FoxD5 in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

13 Samples

Download data: TXT

(Submitter supplied) Morpholino injections were performed to investigate transcriptional targets of Klf2a, and Klf2b in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

8 Samples

Download data: TXT