GEO DataSets

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

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL15472 GPL13741

9 Samples

Download data

(Submitter supplied) We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morpholino anti-sense oligo against Foxh1.

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13741

4 Samples

Download data: TXT

(Submitter supplied) We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 are critical in mesendoderm specification program.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13741 GPL15472

5 Samples

Download data: TXT

(Submitter supplied) Maternally expressed proteins function in vertebrates to establish the major body axes of the embryo, and to establish a pre-pattern that sets the stage for later acting zygotic signals. This pre-pattern drives the propensity of Xenopus animal cap cells to adopt neural fates under various experimental conditions. Previous studies found that the maternally expressed transcription factor, encoded by the Xenopus achaete-scute like gene ascl1, is enriched at the animal pole. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18936

6 Samples

Download data: TXT

(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) We examined the binding dynamics of the maternal TF Foxh1 over a time course of germ layer development. Foxh1 binding was compared to the onset of zygotic transcription (RNA pol II), binding of the co-repressor Tle, Nodal signaling (Smad2/3) and the zygotic endoderm TF Foxa.

Organism:

Xenopus tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL21875

11 Samples

Download data: BED, BEDGRAPH

(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) 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) 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:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

30 Samples

Download data: BW

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

18 Samples

Download data: TXT

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW

(Submitter supplied) We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription factor E2a (E2a-MO). We also characterized gene expression in control and E2a-depleted embryos by RNA-Seq. For ChIP-Seq, three biological replicates of E2a-MO were performed, and two biological replicates of Control embryos were performed. For RNA-Seq, two biological replicates of E2a-MO were performed, and two biological replicates of Control embryos were performed, and the mean expression levels of each gene were compared.

Organism:

Xenopus tropicalis

Type:

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

Platforms:

GPL15472 GPL9320

11 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