GEO DataSets

(Submitter supplied) Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL9062 GPL10977

16 Samples

Download data: CEL, TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: methylcytosine ChIP-chip on tiling array

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10977

4 Samples

Download data: CEL, TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput transcriptome sequencing

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput small RNA sequencing

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

Download data: TXT

(Submitter supplied) Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by genome tiling array

Platform:

GPL1979

24 Samples

Download data: CEL

(Submitter supplied) Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array; Methylation profiling by array

Platforms:

GPL1979 GPL1980

18 Samples

Download data: CEL

(Submitter supplied) Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL19580

9 Samples

Download data: FA, SAM

(Submitter supplied) RNAseq profiling of eight transcription factor mutants during germination in Arabidopsis, at 24 h in the light (after 48h of stratification).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

18 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17311 GPL19580

102 Samples

Download data: SAM

(Submitter supplied) sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17311

30 Samples

Download data: TXT

(Submitter supplied) RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17311

30 Samples

Download data: TXT

(Submitter supplied) methylC-seq profiling of 4 time points during germination in Arabidopsis, from mature seed, through stratification, germination and to post-germination.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17311

15 Samples

Download data: TXT

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

(Submitter supplied) 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL26208 GPL21785

58 Samples

Download data: BED, BW

(Submitter supplied) Whole genome bisulfite sequencing was performed on Chromomethylase-2 and Dicer-like-3 knockout mutants in order to confirm the results from genome wide association mapping and to identify the respective genomic regions that they target.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) Plants display remarkable developmental and phenotypic plasticity in order to adapt to their environment. It has long been postulated that epigenetics plays a key role in these processes, but with one or two exceptions, solid evidence for the role of epigenetic variation in these processes is lacking. A key impediment to understanding these processes is the lack of information on the extent of epigenetic variation and how it relates to genetic and phenotypic variation in natural population, both over the lifecycle of an individual, and over evolutionary time. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

113 Samples

Download data: CSV

(Submitter supplied) We investigated DNA methylation variation in Swedish Arabidopsis thaliana accessions. We found that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is associated with genetic polymorphism in trans. Additionally, complementary RNA-Seq data for the Arabidopsis accessions were used to correlate methylation changes with gene expression across environments.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11221

323 Samples

Download data: TXT

(Submitter supplied) Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions, demonstrating that methylation of transposable elements is temperature sensitive and associated with genetic polymorphism in both cis and trans, whereas gene body methylation is highly correlated with climate of origin and associated with genetic polymorphism in trans that shows evidence of local adaptation. While genome-wide surveys of naturally occurring DNA methylation have been published previously, the degree of genetic control revealed here is unprecedented. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

284 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17639 GPL13222

15 Samples

Download data: TSV