GEO DataSets

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26322

45 Samples

Download data: TSV

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

Organism:

Populus trichocarpa

Type:

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

Platform:

GPL26322

85 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26322

15 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26322

10 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

15 Samples

Download data: TSV

(Submitter supplied) Heritable changes in cytosine methylation can arise stochastically in plant genomes independently of DNA sequence alterations. These so-called ‘spontaneous epimutations’ appear to be abyproduct of imperfect DNA methylation maintenance during mitotic or meitotic cell divisions. Accurate estimates of the rate and spectrum of these stochastic events are necessary to be able to quantify how epimutational processes shape methylome diversity in the context of plant evolution, development and aging.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

13 Samples

Download data: TSV

(Submitter supplied) Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL19580

19 Samples

Download data: TXT

(Submitter supplied) From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139 007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3'-end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three-quarters of the predicted c. more...

Organism:

Populus trichocarpa x Populus deltoides; Populus

Type:

Expression profiling by array

Platform:

GPL5921

10 Samples

Download data: TIFF

(Submitter supplied) In this study, we aimed to characterize the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

44 Samples

Download data: TXT

(Submitter supplied) The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of the genes that play specialized functions during each of these phases of growth Keywords: Developmental series

Organism:

Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL7424

10 Samples

Download data: PAIR

(Submitter supplied) Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

22 Samples

Download data: TXT