GEO DataSets

(Submitter supplied) Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. more...

Organism:

Oryza sativa Japonica Group; Solanum lycopersicum; Solanum pennellii; Medicago truncatula

Type:

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

8 related Platforms

231 Samples

Download data: BED, BW, TXT, XLSX

(Submitter supplied) Legume GRAS-type transcription factors NSP1 and NSP2 are essential for Rhizobium Nod factor-induced nodulation. Both proteins are considered to be Nod factor response factors regulating gene expression upon symbiotic signalling. However, legume NSP1 and NSP2 can be functionally replaced by non-legume orthologs; including rice (Oryza sativa) OsNSP1 and OsNSP2. This shows that both proteins are functionally conserved in higher plants, suggesting an ancient function that was conserved during evolution. more...

Organism:

Sinorhizobium meliloti; Medicago sativa; Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL4652

9 Samples

Download data: CEL

(Submitter supplied) Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL4105 GPL4106

20 Samples

Download data: GPR

(Submitter supplied) Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. more...

Organism:

Rorippa sylvestris; Arabidopsis thaliana; Rorippa amphibia x Rorippa sylvestris; Rorippa amphibia

Type:

Genome variation profiling by array

Platform:

GPL198

20 Samples

Download data: CEL

(Submitter supplied) The WRKY gene family has a very ancient origin but has faced extensive duplication only in the plant kingdom so much that Arabidopsis (Arabidopsis thaliana) has 74 copies of WRKY genes encoding transcription factors while 109 can be found in Rice (Oryza sativa L.). Several studies in the last decade has pointed their involvement in an heterogeneous number of biological processes, from development to hormone signalling, dormancy and senescence, but a wide number of WRKY genes are transcriptionally regulated during biotic or abiotic stresses. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL4315

40 Samples

Download data: GPR

(Submitter supplied) The transcriptional regulatory structure of plant genomes remains poorly defined relative to that of animals. It has been unclear how many cis-regulatory elements generally exist in plant genomes, where these elements lie in relation to their target promoters, and how these features are conserved across species. We employed the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) in four different plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. more...

Organism:

Oryza sativa; Medicago truncatula; Arabidopsis thaliana; Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

15 Samples

Download data: BED

(Submitter supplied) Purpose: To understand the dynamic salt-sress response in Arabidopsis and Marchantia

Organism:

Marchantia polymorpha; Arabidopsis thaliana; Oryza sativa Japonica Group

Type:

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

5 related Platforms

80 Samples

Download data: BW, XLSX

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at variable light and temperature conditions under greenhouse environment (period March-June). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

16 Samples

Download data: PAIR

(Submitter supplied) Comparison of transcriptomes of WT and abi3 mutant lines at 32 and 40 days after pollination

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

12 Samples

Download data: PAIR

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

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

104 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 20/18°C 16 h light/dark, in osmotic stress conditions (-0.1 Mpa). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

16 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 14/11°C, 16h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

20 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at variable light and temperature conditions under greenhouse environment (period March-June). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

20 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 26/24°C 16 h light/dark. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

16 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 21-19°C, 16h light. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

32 Samples

Download data: PAIR

(Submitter supplied) ABI3 is a B3-domain transcription factor that acts as a master regulator of seed maturation. To identify genes that are regulated by this transcription factor in the model legume Medicago truncatula, Medicago hairy roots were generated using Agrobacterium rhizogenes transformed with the genomic sequence of the ABI3 gene of Medicago. Using the Medicago NimbleGen chip, a transciptomic analysis was performed to identify differentially expressed genes compared to the GUS expressed control.

Organism:

Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL16373

6 Samples

Download data: PAIR

(Submitter supplied) Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

36 Samples

Download data: TXT

(Submitter supplied) Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions.  Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of  recovery, relative to control roots. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL22250 GPL26083

238 Samples

Download data: XLSX

(Submitter supplied) In this study, we provide a global overview of genome-wide OsHOX24 binding sites in rice under control and desiccation stress conditions in wild-type and OsHOx24 overexpressing rice plants (H49 line) via chromatin immunoprecipitation sequencing (ChIP-sequencing) approach. We identified numerous downstream targets of OsHOX24 under desiccation stress and control by analyzing the comprehensive binding site map of OsHOX24 at whole genome level in rice.

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9316

16 Samples

Download data: BED

(Submitter supplied) time-course salt stress experiment of model legume Medicago truncatula roots using Affymetrix Medicago Array, aimed to dig some useful gene for improve salt resistance for legumes and other crops

Organism:

Sinorhizobium meliloti; Medicago sativa; Medicago truncatula

Type:

Expression profiling by array

Platform:

GPL4652

12 Samples

Download data: CEL, CHP