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Items: 1 to 20 of 803

1.

Nitrogen source effect (ammonium and nitrate) on Brachypodium distachyon B21 root transcriptome

(Submitter supplied) Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17337
6 Samples
Download data: CSV
Series
Accession:
GSE275962
ID:
200275962
2.

Epigenomic profiles of Brachypodium distachyon mutants deficient in RNA polymerase IV (Pol IV)

(Submitter supplied) Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33763
6 Samples
Download data: TSV
Series
Accession:
GSE243693
ID:
200243693
3.

Transcriptome analysis of the jmj1 mutant

(Submitter supplied) To investigate the effects BdJMJ1 on gene transcription at a genome-wide level
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33763
4 Samples
Download data: TXT
Series
Accession:
GSE243213
ID:
200243213
4.

ChIP-seq to test histone methylation in Bd21-3 and the jmj1-1 mutant.

(Submitter supplied) To investigate the impact of BdJMJ1 on H3K4me1, H3K4me2, H3K4me3, and H3 at the genome-wide level.
Organism:
Brachypodium distachyon
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL33763
20 Samples
Download data: BIGWIG
Series
Accession:
GSE243212
ID:
200243212
5.

differential expression analysis to hight co2 of the brachypodium distachyon-Differential expression of project NGS20_04_HIPATH

(Submitter supplied) ngs2020_04_hipath-differential expression analysis to hight co2 of the brachypodium distachyon-Analysis response of the Brachypodium distachyon to hight CO2 -treatment hight CO2
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
9 Samples
Download data: TXT
Series
Accession:
GSE229886
ID:
200229886
6.

Centromere evolution in Brachypodium genomes with different polyploid levels

(Submitter supplied) Centromeric repetitive DNA sequences are highly variable during evolution, which are the hub for genome stability in almost all the eukaryotic organisms. However, how centromeric repeat sequences diverge rapidly among closely related species and populations, and how polyploidy contributed to the diversity of centromere among co-evolved subgenomes are largely unknown. Here, we applied the Brachypodium system to investigate the track of centromere evolution within this taxa, and their adaptation to alloploidization process. more...
Organism:
Brachypodium distachyon; Brachypodium hybridum; Brachypodium stacei
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL29084 GPL17337 GPL29083
12 Samples
Download data: BED
Series
Accession:
GSE157143
ID:
200157143
7.

Transcriptomic study (RNAseq) of diurnal expression of Brachypodium distachyon ecotypes Bd21 and Bd21-3 under submergence stress

(Submitter supplied) To study the diurnal transcriptome (RNA-seq) expressed by the monocot model plant B. distachyon under submergence stress, we analyzed two different ecotypes (Bd21, submergence sensitive; Bd21-3, submergence tolerant) at 5 different time points (dawn, ZT0; midday, ZT8; dusk, ZT16; middnight ZT20, end of night, ZT24).
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
89 Samples
Download data: XLSX
Series
Accession:
GSE215159
ID:
200215159
8.

Comparative RNA-sequencing of Brachypodium distachyon wild-type and bdmute mature leaf zones

(Submitter supplied) Comparative RNA-sequencing of the mature leaf zones in Brachypodium distachyon wild type and bdmute mutants that do not form stomatal subsidiary cells was performed. The aim was to identify genes relevant for subsidiary cell function in B. distachyon.
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
6 Samples
Download data: CSV
Series
Accession:
GSE206682
ID:
200206682
9.

Comparative RNA-sequencing of Brachypodium distachyon wild-type and bdmute developing leaf zones

(Submitter supplied) Comparative RNA-sequencing of the developmental leaf zones in Brachypodium distachyon wild type and bdmute mutants that do not form stomatal subsidiary cells was performed. The aim was to identify genes relevant for subsidiary cell formation in B. distachyon.
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
6 Samples
Download data: CSV
Series
Accession:
GSE201294
ID:
200201294
10.

Global gene expression in Brachypodium during embryo development

(Submitter supplied) We present an atlas of global gene expression of embryo, endosperm and seed coat in Branypodium, providing insights into the evolution of gene expression in embryogenesis.
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17337
20 Samples
Download data: XLSX
Series
Accession:
GSE168154
ID:
200168154
11.

Effects of karrikins and the strigolactone analogue GR24 on the transcriptome of Brachypodium distachyon seedlings

(Submitter supplied) Objective: to compare and contrast the effects of exogenous application of karrikins KAR1 and KAR2, and the strigolatone analogue rac-GR24, on gene expression in shoot tissue of seedlings of Brachpodium distachyon (false brome). The experiment compared the effects on three genotypes: wild type Bd21-3, and two mutant alleles for the Brachypodium orthoologue of the karrikin receptor KARRIKIN INSENSITIVE2 (KAI2; Bradi1g15880.1). more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
36 Samples
Download data: TXT, XLSX
Series
Accession:
GSE174000
ID:
200174000
12.

microdissection data of 3 vascular bundles stages - Brachypodium Vascular ontogeny

(Submitter supplied) ngs2015_19_anr-jc-bravo-microdissection data of 3 vascular bundles stages-what genes regulate vascular differentiation -Total RNA from microdissected Vascular Bundles at 3 different stages are compared together. They are also compared to the transcriptome with ground tissue. Plant were grown during 15 days. Meristems were sectionned with a freezing microtome. Appropriate vascular bundles were microdissected and catupulted in tubes and appropriates buffer for RNA extraction. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17337
12 Samples
Download data: TXT
Series
Accession:
GSE162395
ID:
200162395
13.

Heterotrimeric G-protein interactions are conserved despite regulatory element loss in some plants

(Submitter supplied) Purpose: To study the shared transcriptional network between suppression transgenic plants of BdG and overexpresssion plants of SiRGS in B. distachyon. Method: Total RNA was isolated from 2 independent transgenic lines of amiR-BdG and Bd-SiRGS-OE. RNA-seq library preparation, sequencing and initial quality control analysis were performed by Novogene Inc. The sequences were analyzed for quality using FastQC. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17337
18 Samples
Download data: CSV, H5, TSV
Series
Accession:
GSE153188
ID:
200153188
14.

Brachypodium distachyon identification of MeJA responsive genes in wild type and MTL-overexpression plants

(Submitter supplied) Plants were treated with MeJA and mRNA was extracted and sequenced
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17337
8 Samples
Download data: TXT
Series
Accession:
GSE124493
ID:
200124493
15.

Iron deficiency response of interactions between Brachypodium and Pseudomonas fluorescens SBW25 under controlled growth conditions.

(Submitter supplied) The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.
Organism:
Pseudomonas fluorescens; Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29167 GPL29168
30 Samples
Download data: TXT
Series
Accession:
GSE158273
ID:
200158273
16.

RNA-Seq profiling of ELF3 and PRR37 in Brachypodium Distachyon

(Submitter supplied) Daylength is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of daylength perception and signal transduction in many systems are not well understood. In trees, photoperiod perception plays a major role in growth cessation during the autumn as well as activating the resumption of shoot growth in the spring, both processes controlled by FLOWERING LOCUS T2 (FT2) expression levels and critical for the survival of perennial plants over winter. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23254
149 Samples
Download data: BW, TXT
Series
Accession:
GSE147373
ID:
200147373
17.

ChIP-Seq profiling of ELF3,PRR37 and PHYC in response to photoperiod change at different ZTime in Brachypodium distachyon

(Submitter supplied) Daylength is an important seasonal cue, and genetic variation in the regulation of photoperiodism has been selected for in adapting wheat and barley to northern latitudes. Despite the importance of this trait, the mechanism by which monocot plants sense photoperiod is not known. We find in Brachypodium distachyon that photoperiodism is mediated by phytochromeC (phyC), a chromophore that acts as a molecular timer and measures the length of the night. more...
Organism:
Brachypodium distachyon
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL23254 GPL29167
11 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE128206
ID:
200128206
18.

vasc1-bravo-Transciptome of VASC1

(Submitter supplied) 4plex_brachy_2016_01 - vasc1-bravo - Are hormone signaling genes misregulated in VASC1. - During a screening of the Brachypodium mutant collection at Versailles, a line was identified with a marked vascular phenotype. The causal locus segregates Mendelian way (a recessive locus). A candidate gene was identified by ILLUMINA sequencing at the Joint Genome Institute (JGI) and by the ShoreMAP technique. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by array
Platform:
GPL27542
8 Samples
Download data: GPR
Series
Accession:
GSE139323
ID:
200139323
19.

The prevalence, evolution and chromatin signatures of plant regulatory elements

(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:
Eutrema salsugineum; Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza; Oryza sativa; Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
13 related Platforms
170 Samples
Download data: BW
Series
Accession:
GSE128434
ID:
200128434
20.

Time-Dependent Transcriptome Profiling Reveals the Importance of Multiple Transcription Factors in Brachypodium Root Development

(Submitter supplied) The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. more...
Organism:
Brachypodium distachyon
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21050
12 Samples
Download data: GTF, XLSX
Series
Accession:
GSE131582
ID:
200131582

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