GEO DataSets

(Submitter supplied) Inferring phenotypic outcome from genomics features is the promise and challenge for basic and applied research. Functionally testing whether the feature(s) with predictive power can shed light on the underlying mechanism remains largely unexplored. We address these gaps by applying a machine learning approach to predict phenotypes based on transcriptome data. We validate the predictive models in silico using out-of-sample varieties and in planta by reverse genetics. more...

Organism:

Arabidopsis thaliana; Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL24163

199 Samples

Download data: TXT

(Submitter supplied) We have characterized the transcriptional response in Maize under limiting and sufficient nitrogen conditions, and have identified a set of genes whose expression profiles can quantitatively assess the response of plants to those conditions.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL14616

90 Samples

Download data: CEL

(Submitter supplied) In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL198 GPL2025

16 Samples

Download data: CEL

(Submitter supplied) The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media and after 10 days protoplasts were generated from root tissue, Cells were transfected with a vector containing the GR-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

56 Samples

Download data: CSV

(Submitter supplied) Maize LEAFBLADELESS1 (LBL1) and Arabidopsis SUPPRESSOR OF GENE SILENCING3 (SGS3) play orthologous roles in the biogenesis of 21 nucleotide trans-acting short-interfering RNAs (tasiRNAs). The phenotypes conditioned by mutation of lbl1 and SGS3 are, however, strikingly different, suggesting that the activities of these small RNA biogenesis components, or the tasiRNAs and their targets might not be entirely conserved. more...

Organism:

Zea mays

Type:

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

Platforms:

GPL13977 GPL15463

10 Samples

Download data: TXT, XLS

(Submitter supplied) Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. A wealth of archeological and population genetic data has established maize as a model system for studying domestication , genome evolution and the genetics and evolution of complex traits. We used expression profiling of 18,242 genes for 38 diverse maize genotypes and 18 teosinte genotypes to examine how domestication has re-shaped the transcriptome of maize seedlings. more...

Organism:

Zea mays; Zea mays subsp. parviglumis

Type:

Expression profiling by array

Platform:

GPL13736

94 Samples

Download data: PAIR

(Submitter supplied) Cis-regulatory elements (CREs) encode the genomic blueprints for coordinating the spatiotemporal regulation of gene transcription programs necessary for highly specialized cellular functions. To identify cis-regulatory elements underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in an atlas of Zea mays tissues and organs. more...

Organism:

Zea mays; Arabidopsis thaliana

Type:

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

Platforms:

GPL25410 GPL26208

14 Samples

Download data: TXT

(Submitter supplied) Coordinated functioning of the cob and florets of the maize ear confers grain yield. However, comprehensive molecular differentiation of the cob and florets and their responses to low nitrogen (LN) stress remain elusive. We compared transcriptional profiles of the cob and peripheral florets of a maize hybrid at the silking stage at two N levels in the field and found 1,864 differentially expressed genes between the cob and florets, with 1314 genes up-regulated in the cob and 550 genes up-regulated in florets. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: TXT

(Submitter supplied) In this study expression levels of 732 genes were analyzed for European maize (Zea mays L.) inbred lines (4 Flint and 5 Dent) and nine corresponding hybrids by microarray analysis. The selection of the 732 genes was based on a previous study (Thiemann et al., Theor Appl Genet 2010, 120:401-413), which sequences were derived from the 46k microarray (platform GPL6438) (University of Arizona, USA). 558 of the 732 genes represented on the microarray were differentially expressed between the original 21 parental inbred lines and were correlated with at least one of the three characteristics MPH (mid-parent heterosis) and/or HP (hybrid performance) of the trait GY (grain yield) and/or HP of the trait grain dry matter content. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL17936

105 Samples

Download data: GPR, TXT

(Submitter supplied) Arabidopsis plants grown in a hydroponic media with sufficient Nitrogen were given a 60mM supply of Nitrogen. Triplicate sets of plants were sampled at time points 0,5,10,15,20,30,45,60,90 and 120 minutes after supply from treated and control plants (20mM KCl). The samples were flash frozen in liquid N and used to construct RNA-Seq libraries to assay transcriptional changes in the shoots and roots, separately, in response to Nitrogen.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

114 Samples

Download data: TXT

(Submitter supplied) Although urea is the most used nitrogen fertilizer worldwide, little is known on the capacity of crop plants to use urea per se as a nitrogen source for development and growth. To date, the molecular and physiological bases of its transport have been investigated only in a limited number of species. In particular, up to date only one study reported the transcriptomic modulation induced by urea treatment in the model plant Arabidopsis (Mérigout et al., 2008 doi: 10.1104/pp.108.119339). more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL17540

12 Samples

Download data: PAIR, TXT

(Submitter supplied) Nitrogen availability in the soil is a major determinant of crop yield. While the application of fertilizer can substantially increase the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing the nitrogen use efficiency in crop plants is a necessary step to implement low input agricultural systems. We exploited the genetic diversity present in the world-wide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, with the aim to identify biomarkers associated with good plant performance under low nitrate availability. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

72 Samples

Download data: CEL

(Submitter supplied) The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with expression regulated by the circadian clock, transcript levels in the aerial tissues of young maize seedlings were determined by transcriptional profiling with the Affymetrix GeneChip Maize Genome Array. Maize inbred B73 seedlings were grown inside Conviron growth chamber. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

12 Samples

Download data: CEL

(Submitter supplied) Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL15621 GPL13499

13 Samples

Download data: PAIR