GEO DataSets

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

Organism:

Branchiostoma lanceolatum; Danio rerio; Oryzias latipes

Type:

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

7 related Platforms

217 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Danio rerio

Type:

Other

Platform:

GPL14875

83 Samples

Download data: BEDGRAPH

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Branchiostoma lanceolatum; Danio rerio; Oryzias latipes

Type:

Expression profiling by high throughput sequencing

4 related Platforms

81 Samples

Download data: TXT

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24206

7 Samples

Download data: BEDGRAPH

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Danio rerio; Branchiostoma lanceolatum; Oryzias latipes

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

29 Samples

Download data: BED

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Branchiostoma lanceolatum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24206

17 Samples

Download data: BED

(Submitter supplied) To be able to fully comprehend the contribution of the epigenome to embryonic development, it is important to understand how various components of the epigenome evolved. To date, a number of studies have thoroughly described various epigenetic mechanisms in both vertebrates and invertebrates, however there is currently a lack of high resolution epigenomic data corresponding to animals that form the invertebrate-vertebrate boundary. more...

Organism:

Branchiostoma lanceolatum

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL23852 GPL25186

10 Samples

Download data: TSV, TXT

(Submitter supplied) Comparison among vertebrates and the cephalochordate amphioxus Hox clusters architectures

Organism:

Danio rerio; Branchiostoma lanceolatum

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14875 GPL20177

74 Samples

Download data: BEDGRAPH, BW, FA

(Submitter supplied) Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation [Pires-daSilva & Sommer, Nat. Rev. Genet. 4, 39-49 (2003)]. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development [Sanz-Ezquerro, Münsterberg & Stricker, Front. more...

Organism:

Xenopus tropicalis; Ptychodera flava

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31011 GPL31012

18 Samples

Download data: TSV

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

Organism:

Branchiostoma lanceolatum; Xenopus tropicalis; Danio rerio; Ptychodera flava

Type:

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

4 related Platforms

75 Samples

Download data: TSV, TXT

(Submitter supplied) Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. more...

Organism:

Danio rerio; Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24210 GPL21741

33 Samples

Download data: TXT

(Submitter supplied) Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. more...

Organism:

Branchiostoma lanceolatum; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24210 GPL21741

24 Samples

Download data: BED

(Submitter supplied) The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These enhancers are linked to developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. more...

Organism:

Danio rerio; Xenopus tropicalis; Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

30 Samples

Download data: BED, TXT

(Submitter supplied) We compared the transcriptomes of Amphioxus (Branchiostoma lanceolatum) control and SU5402 treated embryos to define putative FGF signalling pathway target genes during somitogenesis. Embryos were treated with 50µM of SU5402 from 5.5hpf to 8.5hpf, 11.5hpf, and 14.5hpf or from 15hpf to 18hpf, 21hpf, 24hpf. Total RNA was extracted from control and treated embryos.

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25775 GPL20177

24 Samples

Download data: FASTA, TXT

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...

Organism:

Nematostella vectensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17090

123 Samples

Download data: FASTA, TXT

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19892

165 Samples

Download data: TAB

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

Organism:

Danio rerio; Mnemiopsis leidyi; Nematostella vectensis; Schmidtea polychroa; Hypsibius dujardini; Caenorhabditis elegans; Platynereis dumerilii; Drosophila melanogaster; Amphimedon queenslandica; Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

1143 Samples

Download data: PDF, XLSX

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...

Organism:

Hypsibius dujardini

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19649

126 Samples

Download data: TAB

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...

Organism:

Platynereis dumerilii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19648

97 Samples

Download data: TAB

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...

Organism:

Schmidtea polychroa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19599

132 Samples

Download data: TXT