GEO DataSets

(Submitter supplied) Identification of genes downstream of ta/tbx16 in zebrafish embryos, and identification of direct targets by reference to Ta and Tbx16 ChIP-seq data

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14688

12 Samples

Download data: GPR

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

Organism:

Danio rerio

Type:

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

Platforms:

GPL15583 GPL14688 GPL16509

17 Samples

Download data: GPR, WIG

(Submitter supplied) Identification of Ta and Tbx16 binding sites during gastrulation, and Mixl1 binding sites during endoderm specification

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15583 GPL16509

6 Samples

Download data: WIG

(Submitter supplied) Pbx homeodomain proteins have been implicated in the regulation of gene expression during muscle development. Whether Pbx proteins are required broadly for the regulation of muscle gene expression or are required for the expression of a specific subset of muscle gene expression is not known. We employed microarrays to determine the requirements for Pbx proteins during zebrafish development. Keywords: developmental time course analysis

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL

(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) 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) 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:

GPL6457 GPL14875 GPL9319

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) 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) Complex interplay between cardiac tissues is crucial for their integrity. The flow responsive transcription factor KLF2, which is expressed in the endocardium, is vital for cardiovascular development but its exact role remains to be defined. To this end, we mutated both klf2 paralogues in zebrafish, and while single mutants exhibit no obvious phenotypes, double mutants display a novel phenotype of cardiomyocyte extrusion towards the abluminal side. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL19785

2 Samples

Download data: TXT

(Submitter supplied) We aimed to expand the knowledge of Fgf and Wnt signaling in the zebrafish tailbud. Both pathways are required for proper axis elongation and segmentation and we wished to explore the genes under the control of each pathway during this process. In addition, we saught to identify crosstalk between the two pathways by determining whether pathway effector expression was being changed after time-resolved modification of each pathway using pharmacological modifiers.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

15 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

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

Platforms:

GPL9319 GPL14375

12 Samples

Download data: CALLS, PAIR, WIG, YLF

(Submitter supplied) Here, using ChIP-Seq, we examined the targets of Nanog-like and Mxtx2 in blastula stage zebrafish embryos. We found that Nanog-like bind to its known targets like Oct4, Sox2, and Nanog-like. Nanog-like also bound to genes involved in extraembryonic lineage differentiation, like gata3 and krt4 for EVL differentiation, and mxtx2 and slc26a1 for YSL differentiation, mesoderm specification like ntl and tbx3, cell movement like wnt11 and cxcr4b, and signaling genes like ndr1, bmp2b, fgf8a and wnt8a. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9319

6 Samples

Download data: WIG, YLF

(Submitter supplied) Investigation of whole genome gene expression level changes in nanog-like knockdown embryos , compared to the control-MO injected embryos. Knockdown of nanog-like impaired early gastrulation. To globally analyze which target genes Nanog-like regulates during early embryogenesis, we performed a genome-wide transcription analysis using sphere stage (4 hpf) nanog-like morphants.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14375

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) Understanding the molecular mechanisms controlling early cell fate decisions in mammals is a major objective towards the development of robust methods for the differentiation of human pluripotent stem cells into clinically relevant cell types. Here, we used human embryonic stem cells (hESCs) to study specification of definitive endoderm in vitro. Using a combination of whole genome expression and ChIP-seq analyses, we established a hierarchy of transcription factors regulating endoderm specification. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: BED, GFF, TXT

(Submitter supplied) We identified genome-wide sites of occupancy for the intestine-specific transcription factor ELT-2 in L3-staged N2 worm by performing ELT-2 ChIP-seq on whole worms; we performed RNA-seq on L3-staged N2 whole worms

Organism:

Caenorhabditis elegans

Type:

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

Platforms:

GPL13657 GPL18245

12 Samples

Download data: BED, BW

(Submitter supplied) A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc finger factors and Sox17 HMG domain proteins. While a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. more...

Organism:

Xenopus laevis

Type:

Expression profiling by array

Dataset:

GDS2016

Platform:

GPL1318

31 Samples

Download data: CEL, TXT