GEO DataSets

(Submitter supplied) We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

Organism:

Bombyx mori; Drosophila melanogaster; Callorhinchus milii; Monodelphis domestica; Episyrphus balteatus; Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima; Branchiostoma lanceolatum; Danio rerio; Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum

Type:

Expression profiling by high throughput sequencing

15 related Platforms

89 Samples

Download data: TSV

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

Organism:

Danio rerio; Ptychodera flava; Branchiostoma lanceolatum; Xenopus tropicalis

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:

GPL21741 GPL24210

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Branchiostoma lanceolatum

Type:

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

Platform:

GPL24210

16 Samples

Download data

(Submitter supplied) The goal of this projet was to identify genes differentially expressed between control and Activin-treated explants at two time points (gastrula and neurula stage)

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24210

8 Samples

Download data: TSV

(Submitter supplied) The goal of this projet was to identify genomic region showing differential accessibility between control and Activin-treated amphioxus explants at two time points (gastrula and neurula stage)

Organism:

Branchiostoma lanceolatum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24210

8 Samples

Download data: BED

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

Organism:

Strongylocentrotus purpuratus; Branchiostoma lanceolatum; Danio rerio

Type:

Methylation profiling by high throughput sequencing; Other

5 related Platforms

31 Samples

Download data: BED, BW

(Submitter supplied) Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.

Organism:

Strongylocentrotus purpuratus; Branchiostoma lanceolatum; Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25186 GPL23085 GPL30935

8 Samples

Download data: BW

(Submitter supplied) Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development.

Organism:

Strongylocentrotus purpuratus; Branchiostoma lanceolatum; Danio rerio

Type:

Other

5 related Platforms

15 Samples

Download data: BED

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) 4C-seq experiments to study the evolution of the chromatin architecture of ancient gene regulatory blocks at the origin of vertebrates.

Organism:

Mus musculus; Branchiostoma lanceolatum; Danio rerio

Type:

Other

Platforms:

GPL13112 GPL20177 GPL14875

12 Samples

Download data: BEDGRAPH

(Submitter supplied) The brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this non-canonical form of DNA methylation is evolutionarily conserved. To test this we profile brain cytosine methylation across the major vertebrate lineages, amphioxus, honeybee and octopus, finding that non-CG methylation in adult brain methylomes is restricted to vertebrates. more...

Organism:

Branchiostoma lanceolatum; Danio rerio; Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Lethenteron camtschaticum; Apis mellifera; Callorhinchus milii; Octopus bimaculoides

Type:

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

9 related Platforms

11 Samples

Download data: CGMAP, TSV

(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) 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:

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:

Branchiostoma lanceolatum; Oryzias latipes; Danio rerio

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