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Items: 1 to 20 of 886

1.

Spatial transcriptome of Nematostella vectensis apical organ reveals its molecular signature and associated cells

(Submitter supplied) The spatial transcriptome data has allowed us to explore the differential gene expression among the oral-aboral domains and provided new insights into the apical organ signalling pathways for future mechanistic studies and genes associated with oral/aboral differentiation. This resource identifies numerous candidates for elucidating the functional role of the apical organ and to address the evolution of the metazoan larval nervous system.
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29226
10 Samples
Download data: TXT
Series
Accession:
GSE159166
ID:
200159166
2.

Cyclic dinucleotide stimulation of Nematostella vectensis

(Submitter supplied) In mammals, the cGAS-cGAMP-STING pathway is crucial for sensing viral infection and initiating an anti-viral type I interferon response. cGAS and STING are highly conserved genes that originated in bacteria and are present in most animals. By contrast, interferons only emerged in vertebrates; thus, the function of STING in invertebrates is unclear. Here, we use the STING ligand 2'3'-cGAMP to activate immune responses in a model cnidarian invertebrate, the starlet sea anemone Nematostella vectensis. more...
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29855 GPL29226
33 Samples
Download data: TXT
Series
Accession:
GSE175984
ID:
200175984
3.

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

(Submitter supplied) We performed single-cell transcriptome analysis (using 10x genomics 3' scRNA-seq v3.1 chemistry) in the sea anemone Nematostella vectensis (Cnidaria).
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
1 Sample
Download data: RDS
Series
Accession:
GSE166977
ID:
200166977
4.

Impact of antibiotics, cell-free supernatant, LPS, and live cells on Nematostella vectensis gene expression

(Submitter supplied) We used bacteria isolated from field samples of Nematostella vectensis to quantify gene expression through comparisons of transcriptomes.
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
76 Samples
Download data: TXT
Series
Accession:
GSE167114
ID:
200167114
5.

Diverse CGG binding proteins across eukaryotes produced by independent domestications of hAT transposons

(Submitter supplied) The human transcription factor (TF) CGGBP1 (“CGG Binding Protein”) is conserved only in amniotes, and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we examine the DNA binding preferences of a wide variety of metazoan CGGBP1-like TFs with this bipartite domain using PBM experiments. The derived motifs are available at ...
Organism:
Acyrthosiphon pisum; Salmo salar; Fundulus heteroclitus; Sparus aurata; Chrysemys picta; Austrofundulus limnaeus; Anabas testudineus; Amphiprion percula; Salarias fasciatus; Locusta migratoria; Crocodylus porosus; Homo sapiens; Rhodnius prolixus; Rhipicephalus appendiculatus; Kryptolebias marmoratus; Nematostella vectensis; Acanthochromis polyacanthus; Hippocampus comes; Hofstenia miamia; Petromyzon marinus; Acipenser ruthenus; Gallus gallus; Erpetoichthys calabaricus; Rhizophagus irregularis; Paramormyrops kingsleyae; Aedes aegypti; Culex quinquefasciatus; Latimeria chalumnae; Cyprinus carpio; synthetic construct; Hucho hucho; Amphiprion ocellaris; Labeo rohita; Mola mola; Sphaeramia orbicularis; Anabarilius grahami
Type:
Other
Platform:
GPL11260
258 Samples
Download data: TXT
Series
Accession:
GSE157085
ID:
200157085
6.

Unravelling the developmental and functional significance of an ancient Argonaute duplication

(Submitter supplied) Knockdown of NveAGO1 and NveAGO2 in Nematostella results in severe developmental defects. NveAGO1 and NveAGO2 immunoprecipitation reveals subfunctionalization for differential miRNA sorting as well as siRNA specialization.
Organism:
Nematostella vectensis
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL23029
30 Samples
Download data: XLSX
Series
Accession:
GSE144203
ID:
200144203
7.

Geographical temperature stress in the sea anemone Nematostella vectensis

(Submitter supplied) Gene expression of Nematostella vectensis from 5 different locations under chronic (30 day) temperature stress
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
52 Samples
Download data: TXT
Series
Accession:
GSE144104
ID:
200144104
8.

Gene expression during recovery from different forms of trauma in the sea anemone, Nematostella vectensis

(Submitter supplied) We exposed N. vectensis to three forms of trauma (streptomycin, cytochalasin D, or calcium-free seawater) to determine differences in gene expression during recovery from the trauma. Gene expression was monitored during different time points of recovery for animals exposed to cytochalasin D or calcium-free seawater. Gene expression was monitored following designated times of exposure and after 1 hour of recovery for animals exposed to streptomycin.
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
84 Samples
Download data: TXT
Series
Accession:
GSE144080
ID:
200144080
9.

Global temporal gene expression of Nematostella vectensis in-situ

(Submitter supplied) We assessed genome-wide temporal transcript expression patterns in the sea anemone, Nematostella vectensis, in Great Sippewissett Marsh in Massachusetts, where anemones experienced a natural light cycle with intensity varying from 0-200 lum/ft2, daily temperature fluctuations of ~9C. We measured ‘in situ’ gene expression from recaptured anemones every hour from 0800 to 1700 and identified six time-dependent gene clusters, represented by several genes involved in metabolism, stress, and transcription-translation related functions.
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
66 Samples
Download data: TXT
Series
Accession:
GSE143861
ID:
200143861
10.

The evolution of DNA methylation inheritance and programming in animals

(Submitter supplied) DNA methylation has been found throughout animal kingdom, but it is still unclear whether this epigenetic mechanism affects the evolution of genomic elements in animals. Here, we compare the DNA methylomes of gametes and embryos from 7 representative animal species. We find that parental methylomes are propagated to the progeny without significant changes during embryogenesis in cnidarians and insects, but undergo substantial reprogramming in echinoderms, and the reprogramming become more dramatic during deuterostome evolution. more...
Organism:
Apis mellifera; Ciona savignyi; Strongylocentrotus purpuratus; Nematostella vectensis
Type:
Methylation profiling by high throughput sequencing
4 related Platforms
22 Samples
Download data: BED
Series
Accession:
GSE73545
ID:
200073545
11.

Sequencing short capped RNAs captures acute transcription initiation and identifies promoter and distal regulatory elements across eukaryotes from total RNA

(Submitter supplied) The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSS) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than RNA-seq. more...
Organism:
Oryza sativa; Homo sapiens; Mus musculus; Nematostella vectensis; Neurospora crassa; Capsaspora owczarzaki
Type:
Other
10 related Platforms
40 Samples
Download data: BIGWIG, BW, TXT
12.

Convergent evolution of a vertebrate-like methylome in a marine sponge

(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:
Amphimedon queenslandica; Mnemiopsis leidyi; Nematostella vectensis; 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
Series
Accession:
GSE124016
ID:
200124016
13.

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian

(Submitter supplied) We utilized the eyeless sea anemone, Nematostella vectensis, to quantify gene expression differences between different colors of light (red, green, blue) and in constant darkness through comparisons of 96 transcriptomes
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
96 Samples
Download data: TXT
Series
Accession:
GSE132526
ID:
200132526
14.

Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression

(Submitter supplied) We utilized the Nematostella vectensis to quantify gene expression differences and loss during light:dark cycling and immediately after light cue removal through comparisons of 136 transcriptomes Organismal responses to light:dark cycles can result from two general processes: (i) direct response to light or (ii) a free-running rhythm (i.e., a circadian clock). Previous research in cnidarians has shown that candidate circadian clock genes have rhythmic expression in the presence of diel lighting, but these oscillations appear to be lost quickly after removal of the light cue. more...
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
136 Samples
Download data: TXT
Series
Accession:
GSE132202
ID:
200132202
15.

The methyltransferase HEN1 is required for microRNA and piRNA stability as well as larval metamorphosis in Nematostella vectensis

(Submitter supplied) Knockdown of Dicer and PIWI2 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals.
Organism:
Nematostella vectensis
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL23029
12 Samples
Download data: TXT
Series
Accession:
GSE115184
ID:
200115184
16.

The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis

(Submitter supplied) knockdown of HEN1 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals.
Organism:
Nematostella vectensis
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL23029
8 Samples
Download data: TXT
Series
Accession:
GSE110148
ID:
200110148
17.

Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

(Submitter supplied) We performed single-cell transcriptome analysis (using MARS-seq) in the cnidarian Nematostella vectensis. Additionally we performed bulk ATAC-seq experiments on wild-type specimens, as well as ELAV::mOrange reporter transgenic lines (separating ELAV+ and ELAV- cell populations, representing neurons and non-neurons, respectively).
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23029
8 Samples
Download data: BW, TXT, XLSX
Series
Accession:
GSE95723
ID:
200095723
18.

Post transcriptional modifications of miRNAs in the cnidarian Nematostella vectensis

(Submitter supplied) MicroRNAs of bilaterian animals undergo posttranscriptional modifications such as methylation, tailing and trimming that regulate miRNA stability and function. To gain insight on the evolution of miRNA posttranscriptional modification, we studied regulation of miRNA stability by methylation in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister group of Bilateria.
Organism:
Nematostella vectensis
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL23029
30 Samples
Download data: TXT
Series
Accession:
GSE94526
ID:
200094526
19.

Antagonistic BMP–cWNT signaling in the cnidarian Nematostella vectensis reveals insight into the evolution of mesoderm

(Submitter supplied) Using forward transcriptomics, we show that beta-catenin/Tcf signaling and BMP2/4 signaling provide differential inputs into the cnidarian endomesodermal gene regulatory network (GRN) at the onset of gastrulation (24 h postfertilization) in N. vectensis. Surprisingly, beta-catenin/Tcf signaling and BMP2/4 signaling regulate a subset of common downstream target genes in the GRN in opposite ways, leading to the spatial and temporal differentiation of fields of cells in the developing embryo. more...
Organism:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23802
9 Samples
Download data: TXT
Series
Accession:
GSE101604
ID:
200101604
20.

Nematostella vectensis high resolution developmental transcriptomic time-course

(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:
Nematostella vectensis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17090
123 Samples
Download data: FASTA, TXT
Series
Accession:
GSE71086
ID:
200071086
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