GEO DataSets

(Submitter supplied) Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. more...

Organism:

Hydractinia symbiolongicarpus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33396 GPL33397

45 Samples

Download data: TXT

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

Organism:

Hydra vulgaris

Type:

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

Platform:

GPL32331

51 Samples

Download data: BW, TSV

(Submitter supplied) The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system to understand the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration, and H4K20me1 colocalizes with transcriptional activation machinery locally at the β-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32331

30 Samples

Download data: TSV

(Submitter supplied) The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system to understand the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration, and H4K20me1 colocalizes with transcriptional activation machinery locally at the β-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. more...

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32331

15 Samples

Download data: BW

(Submitter supplied) The evolution of the first body axis in the animal kingdom and an extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system to understand the underlying epigenetic mechanisms. We identify that SETD8 is critical for regeneration, and H4K20me1 colocalizes with transcriptional activation machinery locally at the β-catenin bound TCF/LEF binding sites on the promoters of head-associated genes, marking an epigenetic activation node. more...

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32331

6 Samples

Download data: BW

(Submitter supplied) A Zic4-dependent switch in Hydra turns tentacle into foot cells.

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25712

15 Samples

Download data: TXT

(Submitter supplied) Purpose: The mechanisms driving epithelial cell fate decisions to create differentiated body structures (such as tentacles and basal disk) are not understood in Hydra. We explored the role of Wnt signaling targets Zic4 and Sp5 in this process. Methods: RNA sequencing of differentiated body parts (tentacles) upon knockdowns of the candidate transcription factors. Comparison to existing datasets for body part identity and cell lineage. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19551

36 Samples

Download data: TXT

(Submitter supplied) We use single cell RNA-seq from a regeneration time course to identify the molecular and cellular features of Hydra head regeneration

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25713

5 Samples

Download data: CSV

(Submitter supplied) In Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes, we performed RNA-seq and identified genes that are differentially regulated in response to 48 h of treating the animals with the Notch inhibitor DAPT. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27013

36 Samples

Download data: FASTA, TAB

(Submitter supplied) Recent body of evidence demonstrates that extracellular vesicles (EVs) represent the first language of cell-cell communication emerged during evolution. In aquatic environments, transferring signals between cells by EVs offer protection against degradation, allowing delivering of chemical information in high local concentrations to the target cells. The packaging of multiple signals, including those of hydrophobic nature, ensures target cells to receive the same EV-conveyed messages, and the coordination of a variety of physiological processes across cells of a single organisms, or at the population level, i.e. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28733

2 Samples

Download data: TSV

(Submitter supplied) Animals capable of whole-body regeneration can fully restore any tissue lost due to injury. Because different types of injury may require the regeneration of different structures, transcription during whole-body regeneration needs to dynamically adapt to meet the requirements specific to any given injury. However, the regulatory mechanisms responsible for modulating the transcriptional response to injury are poorly understood at the molecular level. more...

Organism:

Hydra vulgaris

Type:

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

Platforms:

GPL28733 GPL25712

113 Samples

Download data: BED, BW, CSV, MATRIX, RDATA

(Submitter supplied) Hydra have a remarkable ability to regenerate after bisection or dissociation. Thus, Hydra is a unique model for studying the mechanisms underlying stemness and self renewal biology. The regeneration of Hyrda offers unique way to investigate molecular mechanisms leading to the establishment of organizer activity during animal development. Here we have investigated the genome-wide occurrence of RNA Polymearse II and Histone H3 in Hydra vulgaris.

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19432

6 Samples

Download data: BED

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

Organism:

Hydra vulgaris

Type:

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

Platform:

GPL25713

101 Samples

Download data: BIGWIG

(Submitter supplied) The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25713

40 Samples

Download data: TXT

(Submitter supplied) The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. more...

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25713

37 Samples

Download data: BIGWIG

(Submitter supplied) The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. more...

Organism:

Hydra vulgaris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25713

24 Samples

Download data: BIGWIG

(Submitter supplied) Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations, all of which express PIWI proteins; endodermal and ectodermal epithelial stem cells are somatic, whereas the interstitial stem cells have germline competence. more...

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL25712 GPL27013

12 Samples

Download data: TXT

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

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19551

153 Samples

Download data

(Submitter supplied) Transgenics Hydra expressing eGFP in interstitial stem-cells (ISC), gastrodermal epithelial cells (gESC) or epidermal epithelial cells (eESC) were used to sort these populations of stem cells by Fluorescence activated cell sorting (FACS) and perform RNA-seq on enriched populations. The processed data deposited here are also accessible in a graphical manner from a blast-based web interface available at https://hydratlas.unige.ch

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19551

22 Samples

Download data: CSV, FASTA

(Submitter supplied) Treatments targetting fast cycling cells were applied to Hydra in order to: 1. identify compensatory gene expression behaviours after loss of neurogenesis, 2. improve the detection of cell-type expression for all transcripts in Hydra, together with the dataset entitled “Gene expressions in the three Hydra stem cell populations”. The processed data deposited here are also accessible in a graphical manner from a blast-based web interface available at https://hydratlas.unige.ch

Organism:

Hydra vulgaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19551

32 Samples

Download data: CSV, FASTA