GEO DataSets

(Submitter supplied) DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. more...

Organism:

Schistocerca gregaria

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16114

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.

Organism:

Magallana gigas

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13986

2 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

Organism:

Magallana gigas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13986

112 Samples

Download data: BEDGRAPH

(Submitter supplied) Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions. DNA methylation and its role in gene regulation is conserved in stramenopile.

Organism:

Phaeodactylum tricornutum

Type:

Methylation profiling by genome tiling array

Platform:

GPL17291

3 Samples

Download data: PAIR, TXT

(Submitter supplied) Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. more...

Organism:

Physcomitrium patens; Phycomyces blakesleeanus; Drosophila melanogaster; Apis mellifera; Laccaria bicolor; Uncinocarpus reesii; Selaginella moellendorffii; Postia placenta; Ciona intestinalis; Tetraodon nigroviridis; Chlorella variabilis; Oryza sativa; Tribolium castaneum; Nematostella vectensis; Volvox carteri; Coprinopsis cinerea; Bombyx mori

Type:

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

17 related Platforms

33 Samples

Download data: GFF, TXT

(Submitter supplied) To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. more...

Organism:

Daphnia magna; Daphnia pulex

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24022 GPL24021 GPL23821

41 Samples

Download data: TXT, VCF

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

Organism:

Camponotus floridanus; Harpegnathos saltator

Type:

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

4 related Platforms

47 Samples

Download data: BEDGRAPH, FA

(Submitter supplied) Deep BS-Seq of two Ants: Camponotus floridanus and Harpegnathos saltator.

Organism:

Harpegnathos saltator; Camponotus floridanus

Type:

Methylation profiling by high throughput sequencing

4 related Platforms

39 Samples

Download data: TXT

(Submitter supplied) Deep sequencing of mRNA from queen and virgin queen of two Ants: Camponotus floridanus and Harpegnathos saltator

Organism:

Camponotus floridanus; Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14137 GPL14138

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Deep sequencing of smRNA from queen and virgin queen of two Ants: Camponotus floridanus and Harpegnathos saltator

Organism:

Camponotus floridanus; Harpegnathos saltator

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL14138 GPL14137

4 Samples

Download data: FA

(Submitter supplied) Cytosine DNA methylation in the Tribolium castaneum has been controversial, its distribution pattern and functions have not been established yet. Here, using BS-Seq, we confirmed the existence of DNA methylation and described the methylation profiles for four life stages of T.castaneum. Interestingly, two types of DNA methylation had been discovered in T.castaneum genome. One was the symmetrical CpG methylation which was typically existed among eukaryotes methylomes, but occupied small part in methylome of T. more...

Organism:

Tribolium castaneum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL22138

8 Samples

Download data: TAR, TXT

(Submitter supplied) We wanted to infer the contribution of host vs symbiotic microbiota plasticities on thermal acclimation of the holobiont. We long-term acclimated anymals of the same clonal line to 3 different temperatures (15, 20 and 25°C) and monitored along time the changes in fitness, microbiota composition, and host transcriptome.

Organism:

Nematostella vectensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29855

15 Samples

Download data: GFF3, TXT

(Submitter supplied) All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. more...

Organism:

Locusta migratoria

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9308

2 Samples

Download data

(Submitter supplied) To determine whether differences between background strains or housing conditions altered the hepatic methylome, We report the generation and analysis of genome-wide DNA methylation profiles at nucleotide resolution in mouse liver from two male mice on a mixed background (mixed-1, mixed-2) and two males on a pure Black-6 (B6-1, B62) background. Using Enhanced high-throughput Reduced Representation Bisulfite Sequencing (ERRBS), we enriched CpG islands in mouse liver, and covered a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse liver. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) We report the characterized gene body methylation patterns in two Daphnia species.

Organism:

Daphnia pulex; Daphnia magna

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19087 GPL21075

6 Samples

Download data: TXT

(Submitter supplied) Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus’ arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

6 Samples

Download data: TXT

(Submitter supplied) The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. more...

Organism:

Procambarus virginalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24772

3 Samples

Download data: BROADPEAK

(Submitter supplied) The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. more...

Organism:

Procambarus virginalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24771

3 Samples

Download data: TXT

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

Organism:

Procambarus fallax; Procambarus virginalis

Type:

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

Platforms:

GPL22798 GPL24771 GPL24772

26 Samples

Download data: BED, TXT

(Submitter supplied) The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. more...

Organism:

Procambarus fallax; Procambarus virginalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22798 GPL24771

9 Samples

Download data: TXT