GEO DataSets

(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; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus

Type:

Other

30 related Platforms

32 Samples

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

(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:

Mnemiopsis leidyi; Nematostella vectensis; Amphimedon queenslandica; Sycon ciliatum

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:

Mnemiopsis leidyi; Trichoplax adhaerens; Amphimedon queenslandica

Type:

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

Platforms:

GPL24656 GPL21225 GPL22487

10 Samples

Download data: BW, TXT

(Submitter supplied) These data complement GEO accession GSE60478, a time-course of Mnemiopsis leidyi developmental gene expression for hours 0-13 and hour 20. The data here provide additional replicates for 0-13 and 20 hours as well as new timepoints 14–19. As in the original study (Levin et al. 2016 PMID: 26886793) data are from single embryos using the Cel-Seq (Single-Cell RNA-Seq by Multiplexed Linear Amplification PMID:22939981). more...

Organism:

Mnemiopsis leidyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19089

50 Samples

Download data: TXT

(Submitter supplied) A time series from 1 hour to 9 hours post-fertilization (hpf) was collected for RNA-seq by students of the MBL Embryology Course to understand the shifts in gene expression occuring in the early embryo of Mnemiopsis leidyi.

Organism:

Mnemiopsis leidyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19089

31 Samples

Download data: TXT

(Submitter supplied) Ctenophores’ amazing capacity of regeneration has fascinated biologists for centuries. The morphological features of ctenophore regeneration have been documented, but the molecular and cellular components behind this phenomenon have remained a mystery. Here, next generation sequencing technologies and transcriptomic analysis are used to investigate the regeneration dynamics in the ctenophore Mnemiopsis leidyi. more...

Organism:

Mnemiopsis leidyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21225

24 Samples

Download data: XLSX

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

Organism:

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

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:

Mnemiopsis leidyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19089

40 Samples

Download data: TAB