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Items: 1 to 20 of 273

1.

Transcriptomic evolution across bilaterian tissues

(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
Series
Accession:
GSE205498
ID:
200205498
2.

Gain of gene regulatory network interconnectivity at the origin of vertebrates

(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
Series
Accession:
GSE148783
ID:
200148783
3.

Gain of gene regulatory network interconnectivity at the origin of vertebrates [RNA-seq]

(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
Series
Accession:
GSE148782
ID:
200148782
4.

Gain of gene regulatory network interconnectivity at the origin of vertebrates [ATAC-seq]

(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
Series
Accession:
GSE148781
ID:
200148781
5.

Control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

(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
Series
Accession:
GSE166498
ID:
200166498
6.

RNA-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

(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
Series
Accession:
GSE166497
ID:
200166497
7.

ATAC-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

(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
Series
Accession:
GSE166495
ID:
200166495
8.

Base-resolution 5-hydroxymethylcytosine maps of sea urchin and lancelet embryos and adult tissues

(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
Series
Accession:
GSE188334
ID:
200188334
9.

DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq

(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
Series
Accession:
GSE188332
ID:
200188332
10.

Base-resolution DNA hydroxymethylation maps of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using ACE-seq

(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
Series
Accession:
GSE188331
ID:
200188331
11.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(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
12.

Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications

(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
13.

Evolution of CpH methylation in vertebrate brains

(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
Series
Accession:
GSE141609
ID:
200141609
14.

Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos

(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
Series
Accession:
GSE122245
ID:
200122245
15.

Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits

(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
Series
Accession:
GSE106431
ID:
200106431
16.

Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA-Seq]

(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
Series
Accession:
GSE106430
ID:
200106430
17.

Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [CAGE]

(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
Series
Accession:
GSE106429
ID:
200106429
18.

Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ATAC-Seq]

(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
Series
Accession:
GSE106428
ID:
200106428
19.

Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ChIP-Seq]

(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
Series
Accession:
GSE106372
ID:
200106372
20.

Base resolution methylome profiling of Branchiostoma lanceolatum embryos and adult tissues

(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
Series
Accession:
GSE102144
ID:
200102144
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