GEO DataSets

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

Organism:

Arabidopsis thaliana; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL20226

19 Samples

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(Submitter supplied) Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. more...

Organism:

Arabidopsis thaliana; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL20226

7 Samples

Download data: GFF, XLSX

(Submitter supplied) Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.

Organism:

Arabidopsis lyrata subsp. lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

12 Samples

Download data: GFF, XLSX

(Submitter supplied) Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

18 Samples

Download data: BW

(Submitter supplied) Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. more...

Organism:

Oryza sativa Japonica Group

Type:

Other

Platform:

GPL22703

5 Samples

Download data: BW

(Submitter supplied) We have used the genetic resources of Arabidopsis thaliana to generate mutant lines that have reactivated TE expression. We used these lines with long-read Oxford Nanopore sequencing technology to capture Transposable Element (TE) mRNAs for TE transcript annotation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26246

6 Samples

Download data: GFF, TXT

(Submitter supplied) Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similarly to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

17 Samples

Download data: TXT

(Submitter supplied) The main objective of this analysis was to investigate the methylome changes in Arabidopsis plants treated with drugs affecting DNA methylation.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) We report the application of a high-throughput sequencing approach that is specifically designed to analyze the active mobilome of eukaryotes after simultaneous inhibition of RNA polymerase II and/or DNA methylation in O. sativa japonica. We found that the simultaneous inhibition of Pol II and DNA-methylation activated the evolutionary young Houba-Retrotransposon in O. sativa suggesting a crucial role of Pol II in regulating retrotransposition in plants.

Organism:

Oryza sativa Japonica Group

Type:

Other

Platform:

GPL22703

4 Samples

Download data: BIGWIG

(Submitter supplied) Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. more...

Organism:

Saccharum officinarum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15137

1 Sample

Download data: TXT

(Submitter supplied) Heat stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, which however is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. Loss of H1 caused activation of pericentromeric GYPSY elements upon heat treatment, despite that these elements remained highly methylated. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

25 Samples

Download data: TXT

(Submitter supplied) Identification of the newly insertied site of heat-activaed ONSEN transposon on Arabidopsis thaliana

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL14599

6 Samples

Download data: TXT, XLS

(Submitter supplied) To understand an effect of an ONSEN insertion for a gene network, a genome wide gene expression on the ONSEN inserted lines was analyzed by a microarray. The microarray analysis identified 6,520 and 7,262 significant different expressed genes (3/2 fold or 2/3 fold, FDR < 0.05) in 13-7 and 19-4 respectively under ABA stress.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL20796

24 Samples

Download data: TXT

(Submitter supplied) We have sequenced the whole genome of Cleome hassleriana by NGS [SRA accession number SRA058749] and build a reference sequence for this genome. In order to improve quality of gene models, a mix transcriptome sample extracted from the bud, leaf, petiole, stems and flowers of Cleome.

Organism:

Tarenaya hassleriana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16095

1 Sample

Download data: BEDGRAPH

(Submitter supplied) oligo-dT and random primed RNA-seq libraries were used to test an improved annotation of the zebrafish transcriptome

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: CSV

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

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30014 GPL22089

28 Samples

Download data: FASTA, GTF

(Submitter supplied) RNA from brain and fat body/ovary (combined) was sequenced to use in Harpegnathos annotation improvement.

Organism:

Harpegnathos saltator

Type:

Other

Platform:

GPL30014

2 Samples

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(Submitter supplied) This RNA-seq was done separate from any annotation and used to calculate the % of reads mapping to features.

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22089

26 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster; Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22089 GPL19132

49 Samples

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(Submitter supplied) We used 10x Genomics and Drop-seq single-cell RNA-seq to identify the cell type composition of the Harpegnathos brain and study how it changes during the process of adult caste transition (from worker to pseudo-queen), aging, and brain injury.

Organism:

Harpegnathos saltator

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22089

42 Samples

Download data: TXT