GEO DataSets

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

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14376

20 Samples

Download data: TXT

(Submitter supplied) Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14376

10 Samples

Download data: TXT

(Submitter supplied) Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14376

10 Samples

Download data: TXT

(Submitter supplied) Mesoderm differentiation in zebrafish relies on a complex interaction between transcription factors and signaling pathways. Tbx16 is a t-box transcription factor involved in this interaction. Here, we examine downstream targets of tbx16 in the intermediate mesoderm at the 4/5-somite stage and tail mesoderm at the 21-somite stage by comparing wild-type tissues with tissues from the tbx16 mutant, spadetail (spt).

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

11 Samples

Download data: CEL

(Submitter supplied) Using chromatin immunoprecipitation combined with microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by genome tiling array

9 related Platforms

27 Samples

Download data: GPR

(Submitter supplied) The zebrafish genes spadetail (spt) and no tail (ntl) encode T-box transcription factors that are important for early mesoderm development. Although much has been done to characterize these genes, the identity and location of target regulatory elements remain largely unknown. Here, we survey the genome for downstream target genes of the Spt and Ntl T-box transcription factors. We find evidence for extensive additive interactions towards gene activation and limited evidence for combinatorial and antagonistic interactions between the two factors. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7343

12 Samples

Download data: TXT

(Submitter supplied) We integrate zebrafish embryology with photoactivatable caged morpholinos (cMO), the photoactivatable lineage tracer caged fluorescein-dextran (cFD), fluorescence-activated cell-sorting (FACS) and RNA sequencing (RNA-seq) to identify Spadetail-regulated genes in mesodermal cells enriched for early somite progenitors.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

10 Samples

Download data: TXT

(Submitter supplied) Purpose: The goals of this study were to compare the effect on the transcriptome of loss of the Tbx5 paralogues in zebrafish. Methods: Whole embryos were injected with morpholinos targetting either Tbx5a, Tbx5b, or both at the single cell stage. At either 18 or 21 hpf, embryos were pooled and RNA was extracted from the whole embryo. Transcriptomes were generated using Illumina HiSeq 2500. Results: The preliminary experiment produced 632 million reads and a list of 494 differentially expressed genes (detected using Cuffdiff), of which 454 were unique. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

30 Samples

Download data: TXT

(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) 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) Single cell RNA-sequencing analysis of zebrafish embryos with wild type and crispant sample.

Organism:

Danio rerio; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25922 GPL17021

31 Samples

Download data: CSV, MTX, TSV