GEO DataSets

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

Organism:

Phaeodactylum tricornutum

Type:

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

Platform:

GPL30913

9 Samples

Download data: BW, TSV

(Submitter supplied) Loss of DNA methylation is traditionally associated with transcriptional up-regulation of transposable elements. Here we describe for the first time expression changes upon loss of DNA methylation in diatoms using Phaeodactylum tricornutum as a model species. The loss of DNA methylation was obtained by generation of DNMT5 KOs, a divergent DNMT with SNF-like domains. Expression analysis confirm the loss of DNA methylation is associated with de-repression of transposable elements in Phaeodactylum tricornutum with indirect effects on protein coding genes.

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30913

6 Samples

Download data: TSV

(Submitter supplied) DNA methylation has been associated with transcriptional repression of transposable elements. Here we describe the first DNA methylation deficient cell line of a diatom by generating DNMT5:KOs in Phaeodactylum tricornutum. These data show the extend of the loss of DNA methylation in DNMT5:KOs compared to the reference strain. All DNA methylation is lost in DNMT5:KOs.

Organism:

Phaeodactylum tricornutum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30913

3 Samples

Download data: BW

(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) Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq.

Organism:

Phaeodactylum tricornutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20142

10 Samples

Download data: GFF3

(Submitter supplied) Phosphate (Pi) is an essential element to all living cells yet fluctuations in Pi concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton clade living in the world’s oceans adapting to and surviving long periods of sub-optimal conditions and resuming growth as soon as nutrient concentrations permit. The knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19904

10 Samples

Download data: TXT

(Submitter supplied) DNA methylation occurs at preferred sites in eukaryotes, although the basis for preference is not known. We use a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related RNA silencing component (AGO4) in methylating target loci. We find that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL2726 GPL1911

60 Samples

Download data

(Submitter supplied) The only group of organisms in which a biological function for cadmium has been shown is the diatoms, which are unicellular phytoplankton. Yet diatoms exhibit similar sensitivity to Cd as other groups of phytoplankton. We have investigated responses of Cd on molecular, metabolic and physiological levels in the diatom Phaeodactylum tricornutum. P. tricornutum apparently has a high tolerance to Cd; only minor responses were observed on growth, pigment and transcriptional changes at cadmium concentrations of 123 µg/l. more...

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL7021

6 Samples

Download data: GPR

(Submitter supplied) We investigated the effects of extracellular silicic acid on the whole Phaeodactylum triconutum transcriptome. In this work, global transcription analyses were combined with comparative studies of other elements, and detailed analyses of the silicon transporters. Our results provide insight on Si-sensing genes and further extend current models for Si uptake. Keywords: Comparative transcriptome analyses from Phaeodactylum triconutum fusiform cells acclimated in a Si-free or silicic acid medium.

Organism:

Phaeodactylum tricornutum

Type:

Expression profiling by array

Platform:

GPL7021

6 Samples

Download data: GPR, TIFF

(Submitter supplied) Cytosine methylation (5mC) plays a key role in maintaining progenitor cell self-renewal and differentiation. Here, we analyzed the role of 5mC in kidney development by genome-wide methylation and expression profiling and by systematic genetic targeting of DNA methyltransferases (Dnmt) and Tet eleven hydroxylases (Tet). In mice, nephrons differentiate from Six2+ progenitor cells, therefore we created animals with genetic deletion of Dnmt 1, 3a, 3b, Tet1, or Tet2 in the Six2+ population (Six2Cre/Dnmt1flox/flox, Six2Cre/Dnmt3aflox/flox, Six2Cre/Dnmt3bflox/flox, Six2Cre/Tet2flox/flox or Tet1-/-). more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) DNA methylation in basal nematodes analysed by bisulfite sequencing

Organism:

Trichinella spiralis; Romanomermis culicivorax; Trichuris muris; Plectus sambesii

Type:

Methylation profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: BED

(Submitter supplied) Whole genome Bisulfite sequencing

Organism:

Parhyale hawaiensis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21974

1 Sample

Download data: TXT