GEO DataSets

(Submitter supplied) To determine the optimal RNA-Seq approach for animal host-bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available.

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22487

6 Samples

Download data: MATRIX

(Submitter supplied) Marine pelagic larvae from throughout the animal kingdom use a hierarchy of environmental cues to identify a suitable benthic habitat on which to settle and metamorphose into the reproductive phase of the life cycle. The majority of larvae are induced to settle by biochemical cues and many species have long been known to preferentially settle in the dark. Combined, these data suggest that larval responses to light and biochemical cues may be linked, but this is yet to be explored at the molecular level. more...

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26567

43 Samples

Download data: TXT

(Submitter supplied) Vertebrates have highly methylated genomes at CpG positions while most invertebrates have sparsely methylated genomes. Therefore, hypermethylation is considered a major innovation that shaped the genome and the regulatory roles of DNA methylation in vertebrates. However, here we report that the marine sponge Amphimedon queenslandica, belonging to one of the earliest branching animal lineages, has evolved a hypermethylated genome with remarkable similarities to that of a vertebrate. more...

Organism:

Sycon ciliatum; Mnemiopsis leidyi; Nematostella vectensis; Amphimedon queenslandica

Type:

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

5 related Platforms

36 Samples

Download data: CGMAP, TXT

(Submitter supplied) We performed single-cell transcriptome analysis (using MARS-seq) in the sponge Amphimedon queenslandica (adult and larval stages), in the ctenophore Mnemiopsis leidyi (adult stage), and in the placozoan Trichoplax adhaerens (adult stage). Additionally we performed bulk iChIP experiments (2 replicates of each experiment) using antibodies against H3K4me3 and H3K4me2 in adult Mnemiopsis leidyi and adult Trichoplax adhaerens.

Organism:

Trichoplax adhaerens; Amphimedon queenslandica; Mnemiopsis leidyi

Type:

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

Platforms:

GPL24656 GPL22487 GPL21225

10 Samples

Download data: BW, TXT

(Submitter supplied) We deep sequence DNA associated with immunoprecipitated chromatin containing histones with specific post-translational modifications (PTMs) to identify transcriptionally active or repressed regions of the genome of the sponge Amphimedon queenslandica.

Organism:

Amphimedon queenslandica

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18214 GPL22487

20 Samples

Download data: BED, BW

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

Organism:

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

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:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18214

124 Samples

Download data: FASTA, TAB

(Submitter supplied) Transcriptomic data for 59 single embryos and larvae samples of the sponge Amphimedon queenslandica

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18214

59 Samples

Download data: CSV, GTF

(Submitter supplied) Poriferans, like the demosponge Amphimedon queenslandica, are the earliest diverging metazoans and may hold the key to understanding the evolution of metazoan pathways. A. queenslandica exhibits a biphasic lifecycle, with free-swimming larvae and sessile adult stages. To study changes in the transcriptome during this period of morphological and ecological transition, we generated poly(A) fragment libraries for A. more...

Organism:

Amphimedon queenslandica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13724

11 Samples

Download data: WIG

(Submitter supplied) We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon

Organism:

Trichoplax adhaerens; Monosiga brevicollis; Amphimedon queenslandica; Nematostella vectensis

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

17 Samples

Download data: TXT