GEO DataSets

(Submitter supplied) Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). While cis regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low affinity, secondary binding motif, although the primary, high affinity motif is conserved. more...

Organism:

Strongylocentrotus purpuratus; Patiria miniata

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20965 GPL22676

4 Samples

Download data: BED, BEDGRAPH

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

Organism:

Strongylocentrotus purpuratus; Patiria miniata

Type:

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

Platforms:

GPL22676 GPL20965

10 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development. more...

Organism:

Patiria miniata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22676

6 Samples

Download data: TXT

(Submitter supplied) ChIP-seq provides a genome-wide view of the binding sites of Alx1, a pivotal transcription factor in a gene regulatory network that controls skeletogenesis in sea urchins and other echinoderms.

Organism:

Strongylocentrotus purpuratus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20965

2 Samples

Download data: BED, NARROWPEAK

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

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL13304

82 Samples

Download data

(Submitter supplied) Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: BW

(Submitter supplied) Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

80 Samples

Download data: TXT

(Submitter supplied) The transcription factor Pax6 is comprised of the paired domain (PD) and homeodomain (HD). In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific subpopulations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification. Pax6 also regulates the entire lens developmental program. To reconstruct Pax6-dependent gene regulatory networks (GRNs), ChIP-seq studies were performed using lens and forebrain chromatin from mice. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL17021

24 Samples

Download data: BED, NARROWPEAK, TXT