GEO DataSets

(Submitter supplied) The overall objective was to document transcriptomic changes in the guard cells of Thellungiella salsuginea under short (1x) - and long-term (3x) saline growth conditions. For that. microarray analysis was performed using a 60-mer oligonucleotide probe array from Agilent (44 K, design number 031554, Santa Clara, CA, USA). It was clearly observed that salt salinity alters the transcriptomic landscape of Thellungiella guard cells. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by array

Platform:

GPL19319

12 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to profile gene expression changes during flg22 activated pattern-triggered immunity in multiple Brassicaceae including Capsella rubella, Cardamine hirsuta and Eutrema salsugineum as well as in multiple Arabidopsis thaliana accessions. This allows comparative transcriptomics within and across species to investigate the evolution of stress-responsive transcrption changes in these species.

Organism:

Cardamine hirsuta; Eutrema salsugineum; Arabidopsis thaliana; Capsella rubella

Type:

Expression profiling by high throughput sequencing

5 related Platforms

102 Samples

Download data: TXT

(Submitter supplied) Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. more...

Organism:

Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Oryza sativa; Brachypodium distachyon; Eutrema salsugineum; Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza

Type:

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

13 related Platforms

170 Samples

Download data: BW

(Submitter supplied) In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H=A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. more...

Organism:

Eutrema salsugineum

Type:

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

Platform:

GPL21150

41 Samples

Download data: BED, TSV, TXT

(Submitter supplied) Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h) Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.

Organism:

Arabis stelleri; Eutrema salsugineum; Arabidopsis thaliana; Rorippa islandica

Type:

Expression profiling by array

Platform:

GPL26403

23 Samples

Download data: TXT

(Submitter supplied) Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profil-ing and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20016

2 Samples

Download data: XLSX

(Submitter supplied) Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. more...

Organism:

Eutrema salsugineum; Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL16263 GPL9020

36 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...

Organism:

Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii

Type:

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

30 related Platforms

34 Samples

Download data: TSV

(Submitter supplied) In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. more...

Organism:

Arabidopsis thaliana; Capsella rubella; Brassica rapa; Arabidopsis lyrata; Brassica oleracea; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

10 related Platforms

44 Samples

Download data: BED, TSV

(Submitter supplied) Arabidopsis thaliana is a glycophyte with a low salt tolerance, while Eutrema is a halophyte with a very high salt tolerance. To elucidate the transcriptional basis of this difference, we performed hydroponis culture experiments where we grew plants under control conditions (25 mM NaCl) or under salt stress (200 mM NaCl for both species, 500 mM for Eutrema). Salt concentration was increased for the stress treatments by increments of 50 mM per day (25 mM on the first day). more...

Organism:

Arabidopsis thaliana; Eutrema salsugineum

Type:

Expression profiling by array

Platforms:

GPL9020 GPL16263

15 Samples

Download data: TXT

(Submitter supplied) The transcriptional response of T. salsuginea to UV irradiation and AgNO3 was monitored by microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated.

Organism:

Eutrema salsugineum

Type:

Expression profiling by array

Platform:

GPL19319

12 Samples

Download data: TXT

(Submitter supplied) Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. more...

Organism:

Arabidopsis thaliana; Eutrema salsugineum

Type:

Expression profiling by array

Platforms:

GPL16263 GPL9020

24 Samples

Download data: TXT

(Submitter supplied) Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. more...

Organism:

Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17514

10 Samples

Download data: TXT

(Submitter supplied) Thellungiella_8x60K, 4x44K design ID 031554 transfer to 8x60K Arrays of this design have barcodes that begin with 16065426 or 2565426. Protocol: see manufacturer's web site at http://www.agilent.com/

Organism:

Eutrema salsugineum

2 Series

24 Samples

Download data: TXT

(Submitter supplied) Thelungiella 4x44 Hincha Arrays of this design have barcodes that begin with 16031554 or 2531554. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Eutrema salsugineum

3 Series

27 Samples

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