Similar studies for GEO DataSets (Select 200149217) - GEO DataSets

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Items: 15

Select item 2001492171.

Atlas of chromatin accessibility and translatome of tomato and rice root tip cell types

(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

Series

Accession:: GSE149217

ID:: 200149217

PubMed Similar studies SRA Run Selector

Select item 2001590552.

Single cell mRNA-Seq of developing stem-borne roots in tomato

(Submitter supplied) Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29032
1 Sample

Download data: CSV, TXT

Series

Accession:: GSE159055

ID:: 200159055

PubMed Similar studies SRA Run Selector

Select item 2001590503.

Developmental series of tomato lateral root development

(Submitter supplied) The purpose of this dataset is to generate a transcriptomic series of staged non-induced lateral root intiation in M82 tomato. Sections of the primary roots containing lateral roots at 5 different developemental stages (staged by their anatomy and expression of the auxin response marker DR5) were collected.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21762
12 Samples

Download data: CSV

Series

Accession:: GSE159050

ID:: 200159050

PubMed Similar studies SRA Run Selector

Select item 2000855164.

Diversification of Root Hair Development Genes in Vascular Plants

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

Type:: Expression profiling by high throughput sequencing

8 related Platforms
30 Samples

Download data: XLS, XLSX

Series

Accession:: GSE85516

ID:: 200085516

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000636375.

Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

(Submitter supplied) The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by array

Platform:: GPL16358
15 Samples

Download data: CEL

Series

Accession:: GSE63637

ID:: 200063637

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001238196.

Time-series transcript profiling analysis in stem base of rice crown rootless 1 mutant after ectopic expression induction by dexamethasone of the CRL1 gene

(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 ROOTLESS 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; Oryza sativa Japonica Group

Type:: Expression profiling by array

Platform:: GPL25932
96 Samples

Download data: CEL, CHP

Series

Accession:: GSE123819

ID:: 200123819

Select item 2000381027.

Expression data from Oryza sativa and Arabidopsis thaliana

(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

Series

Accession:: GSE38102

ID:: 200038102

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000532728.

Transcript profiling in stem base of crown root less 1 mutant after ectopic expression induction by dexamethasome of CRL1

(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

Series

Accession:: GSE53272

ID:: 200053272

Select item 2000980979.

High-resolution gene expression datasets of ontogenetic zones in the root apical meristem

(Submitter supplied) In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem (RAM), a group of slowly dividing quiescent center (QC) cells is thought to limit stem cell activity to directly neighboring cells (Cowels, 1956; van den Berg et al., 1997), thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction with the more gradual changes in cell division potential (Bennett and Scheres, 2010) and differentiation (Yamaguchi et al., 2008; 2010; Furuta et al, 2014; Geldner, 2013; Masucci et al., 1996; Dolan and Costa, 2001) that occur as cells move further away from the QC. more...

Organism:: Arabidopsis thaliana

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17639
24 Samples

Download data: TXT

Series

Accession:: GSE98097

ID:: 200098097

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006466510.

Conserved Molecular Program for Root Development in Diverse Plants

(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; Zea mays; Oryza sativa

Type:: Expression profiling by high throughput sequencing

7 related Platforms
60 Samples

Download data: CSV

Series

Accession:: GSE64665

ID:: 200064665

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010148211.

ATAC-seq profiling of open chromatin in the root tips of four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) and two Arabidopsis thaliana cell types (root hair and non-hair epidermal cells)

(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:: Medicago truncatula; Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms
15 Samples

Download data: BED

Series

Accession:: GSE101482

ID:: 200101482

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016429712.

Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

(Submitter supplied) Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. more...