GEO DataSets

(Submitter supplied) We report the methylation level of photodamage repair deficient plants 24h upon UV-C exposure. We determined the methlome changes genome wide and at photodamaged sites using NGS approaches.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

31 Samples

Download data: BED, TXT

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

Organism:

Arabidopsis thaliana

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

23 Samples

Download data: GFF

(Submitter supplied) This study reports that the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) form a chromatin-bound complex, which facilitates recognition of photo-lesions.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

16 Samples

Download data: GFF

(Submitter supplied) This study reports that the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) form a chromatin-bound complex, which facilitates recognition of photo-lesions.

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL13222

7 Samples

Download data: GFF

(Submitter supplied) Senescence occurs in a programmed manner to dismantle the vegetative tissues and redirect the nutrients towards metabolic pathways supporting reproductive success. External factors can trigger the senescence program as an adaptive strategy, indicating that this terminal program is controlled at different levels. Using bisulphite conversion followed by sequencing, we interrogated changes in the methylome of senescent Arabidopsis leaves induced by darkness, and their impact on gene and transposable element (TE) expression with transcriptome sequencing. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

8 Samples

Download data: BW, TXT

(Submitter supplied) We used the recently developed Excision Repair-sequencing (XR-seq) method to study genome-wide repair of UV-induced DNA damage in Arabidopsis. We found that the repair of cyclobutane pyrimidine dimers for a large fraction of the genome is controlled by the joint actions of the circadian clock and transcription by RNA polymerase II. Arabidopsis has a relatively compact genome, and a large fraction of the genes are controlled by the circadian clock. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platforms:

GPL21785 GPL17639

16 Samples

Download data: TXT

(Submitter supplied) DNA methylation is one of the most widely distributed epigenetic marks that has a profound impact on developmental regulation, yet its influence on chromatin accessibility and 3D genome architecture is not well explored in plants. Here, we present genome-wide chromatin accessibility profiles of 18 Arabidopsis mutants that are deficient in CG, CHG or CHH DNA methylation. We find that chromatin inaccessibility at heterochromatin regions are maintained by DNA methylation in all three contexts. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL17639

50 Samples

Download data: BW, HIC

(Submitter supplied) Bisulfite treatment libraries were made to characterize the DNA methylome of tea tree

Organism:

Camellia sinensis var. assamica

Type:

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

Platform:

GPL25579

4 Samples

Download data: TXT, WIG

(Submitter supplied) Global genome repair (GGR), a subpathway of nucleotide excision repair (NER), corrects bulky helix-distorting DNA lesions across the whole genome, and is essential for preventing mutagenesis and skin cancer. Here we show that METTL14 (methyltransferase-like 14), a critical component of the m6A RNA methyltransferase complex, promotes GGR through regulating m6A mRNA methylation-mediated DDB2 translation and suppresses UV-induced skin tumorigenesis. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

12 Samples

Download data: BW

(Submitter supplied) Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unravelling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a non-invasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

178 Samples

Download data: TXT

(Submitter supplied) Transcriptome of Arabidopsis thaliana mem1-1 mutant and Col-0 under normal and 200ppm MMS treatment conditions, respectively

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TXT

(Submitter supplied) Improving plant stress response holds great agricultural potential. One promising, yet speculative, possibility is the formation of plant stress memory facilitating enhanced responses to recurring stress. One possibility is the involvement of environmentally-induced variation in reversible chromatin marks, such as DNA methylation, leading to the altered regulation of underlying genetic elements that promote enhanced stress tolerance. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

29 Samples

Download data: BED, COV

(Submitter supplied) These findings reveal the global chromatin response to UV damage and its relation to impaired gene regulation

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

15 Samples

Download data: BED, CSV, TXT

(Submitter supplied) The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeller DDM1 causes hundreds of genomic regions to switch from CMT2-dependency to RdDM-dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17639 GPL23157

42 Samples

Download data: BW, TDF, TSV, WIG

(Submitter supplied) The dominant genetic signature found in melanoma is C to T mutations due to UV radiation. Nucleotide excision repair (NER) recognises and repairs UV-induced DNA damage. We aimed to determine the effect of high UV exposure on the melanoma transcriptome and key NER transcripts in melanoma tumours in association with clinical and genetic features of the disease. 196 primary or metastatic melanomas were utilised for this study. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8432

141 Samples

Download data: TXT

(Submitter supplied) m6A RNA immunoprecipitation experiments were conducted to identify RNAs that are directly m6A-methylated by the METTL3 methylatransferase specifically in response to UV.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

24 Samples

Download data: BED