GEO DataSets

(Submitter supplied) We define genome-wide temporal expression patterns of root development genes in seven vascular plants, enabling a detailed comparative analysis of the molecular development of a single organ across diverse species.

Organism:

Cucumis sativus; Arabidopsis thaliana; Solanum lycopersicum; Selaginella moellendorffii; Glycine max; Oryza sativa; Zea mays

Type:

Expression profiling by high throughput sequencing

7 related Platforms

60 Samples

Download data: CSV

(Submitter supplied) Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). more...

Organism:

Arabidopsis thaliana; Solanum lycopersicum; Zea mays; Oryza sativa; Cucumis sativus; Glycine max

Type:

Expression profiling by high throughput sequencing

8 related Platforms

30 Samples

Download data: XLS, XLSX

(Submitter supplied) We developed a method to synchronize the induction of lateral roots in primary and adventitious roots of Zea mays, and used it to perform a genome-wide transcriptome analysis of the pericycle cells in front of the phloem poles during lateral root initiation.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL16941

30 Samples

Download data

(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) Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

20 Samples

Download data: CEL

(Submitter supplied) Plant species have evolved specialized cell types and regulatory programs. To understand this diversity, we profiled tomato cell type translatomes and chromatin accessibility. While cell type expression signatures are diverse, some genes exhibit robust cell type expression across time and environments. Using xylem differentiation as a model, newly described, repurposed and conserved genes illustrate this spatial variation. more...

Organism:

Solanum lycopersicum; Oryza sativa Japonica Group

Type:

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

Platforms:

GPL21762 GPL25655 GPL21812

145 Samples

Download data: BED, BW, CSV

(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) Trichoderma spp. are versatile opportunistic plant symbionts which can colonize the apoplast of plant roots. Microarrays analysis of Arabidopsis thaliana roots inoculated with Trichoderma asperelloides T203, coupled with qPCR analysis of 137 stress-responsive genes and transcription factors, revealed wide gene transcript reprogramming, preceded by a transient repression of the plant immune responses supposedly to allow root colonization. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

2 Samples

Download data: TXT

(Submitter supplied) RNA-seq expression data was generated for root, shoot, rhizophore, and leaf of S. moellendorffii.

Organism:

Selaginella moellendorffii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23399

8 Samples

Download data: XLSX