GEO DataSets

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

Organism:

Danio rerio

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL9319 GPL6457

16 Samples

Download data: GPR

(Submitter supplied) Study of Smad2 and Eomesa genomic binding in zebrafish blastulas, their relationship to eachother and the relaptionship between genomic binding and Ndr1 and Eomesa responsive genes as identified by microarray and RNA-seq.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TXT

(Submitter supplied) Study of Smad2 and Eomesa genomic binding in zebrafish blastulas, their relationship to eachother and the relaptionship between genomic binding and Ndr1 and Eomesa responsive genes as identified by microarray and RNA-seq.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9319

6 Samples

Download data: TXT

(Submitter supplied) Identification of genes downstream of ndr1 in zebrafish blastulas, and identification of direct targets by reference with Smad2 and Eomesa ChIP-seq data

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

6 Samples

Download data: GPR

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL24995

13 Samples

Download data

(Submitter supplied) We have performed single-cell RNA-seq of cranial NC cells in zebrafish over several stages during their migration

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

7 Samples

Download data: CSV

(Submitter supplied) The purpose of this study was to obtain an unbiased list of wnt-regulated genes in zebrafish neural crest.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TXT

(Submitter supplied) During vertebrate embryogenesis, vascular endothelial cells originate in the lateral plate mesoderm (LPM) next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

2 Samples

Download data: TXT, ZIP

(Submitter supplied) We have developed a method for rapidly identifying early, regionally-expressed molecules: FACS-Assisted Microdissection of Photolabeled cells (FAM-P). For our first FAM-P project, we injected embryos with purified Kaede protein, a stony coral protein that fluoresces at 514 nm (green) prior to- and 582 nm (red) after photoconversion at 405 nm. We used the scanning laser of a confocal microscope to photolabel late blastula-stage embryos along 4-6 tiers of marginal cells, comprising the mesoderm and endoderm germ layer precursors. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL4609

23 Samples

Download data: TXT

(Submitter supplied) In this study, single cell sequencing technique was utilized to explore the transcriptomes of zebrafish PGCs in three time points: 6hpf (shield stage), 11hpf (3-somite stage) and 24hpf (prim-5 stage).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: TXT

(Submitter supplied) Molecular and cellular analysis of mural cell development during zebrafish embryonic development

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20828 GPL14875

17 Samples

Download data: CSV

(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) 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 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) TMEM88 is indispensable for heart development and acts in the pre-cardiac mesoderm to specify lineage commitment of the cardiovascular progenitor cell through inhibition of Wnt signaling.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5077

Platform:

GPL10558

4 Samples

Download data: TXT

Analysis of RUES2 stem cells first depleted for transmembrane protein 88 (TMEM88) and then induced to differentiate into cardiac cells. RUES cells examined at day 5 of differentitation. Results provide insight into the role of TMEM 88 in cardiac cell differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 other, 2 protocol sets

Platform:

GPL10558

Series:

GSE43805

4 Samples

Download data

(Submitter supplied) Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL13318

12 Samples

Download data: CALLS, PAIR

(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