GEO DataSets

(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) 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) Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; Dobrovolskaïa-Zavadskaïa, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981) We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4128 GPL4129

4 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) 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:

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) The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs.

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL19057

20 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10164

4 Samples

Download data: BED, TXT

(Submitter supplied) Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown. We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region. We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16). more...

Organism:

Ciona intestinalis

Type:

Expression profiling by array

Platform:

GPL15657

17 Samples

Download data: CEL

(Submitter supplied) Genetic dissection of the mouse Brachyury locus identified a notochord enhancer and predicts additional control elements essential for trunk and tail development of the mouse embryo.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

1 Sample

Download data: BW

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

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23563 GPL29327

42 Samples

Download data

(Submitter supplied) The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. more...

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29327

15 Samples

Download data: XLSX