E-GEOD-74222
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-74222 | ExpressionAtlas | 2019-01-10
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-74222-analysis-methods.tsv | Tabular | |||
| E-GEOD-74222-analytics.tsv | Tabular | |||
| E-GEOD-74222-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-74222-configuration.xml | Xml | |||
| E-GEOD-74222-g1_g2-mvaPlot.png | Other |
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Project description: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).
2022-10-15 | GSE215159 | GEO
Project description:Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days. Methods (Stress): Brachypodium Bd21 and Bd2-3 plants (14-day-old, 6 leaves stage) were submerged in a water column of 30 cm inside opaque-wall plastic tanks. Light still reached the plants at 40 uE m-2 s-??1. Ecotypes were submerged side-by-side in a randomized manner; only plants submerged in the same tank were compared. Controls were grown in plastic tanks without a water column. Submergence stress started at ZT14 (2h before night, long-day regime 16h light, 8h dark). Above ground tissue was collected after 48 h submergence stress in liquid nitrogen and stored at -80C in an ultra freezer until further processing. Tissue was ground to powder with mortar, pestle and liquid nitrogen avoiding thawing. Control and submerged total RNA was extracted with TRIzol reagent (Invitrogen, 15596018), purified with Direct-zol RNA mini prep columns (Zymo Research, R2050) and digested in-column with DNAse I (ThermoScientific, EN0521). RNA integrity and concentration was verified in denaturing 1.0% agarose gels, Nanodrop 2000 (ThermoScientific) and in a Bioanalyzer 2100 (Agilent) with the integrated software 2100 Expert, samples had a RNA Integrity Number (RIN) between 6.4-7.2 characteristic of aerial plant tissue (Babu and Gassman, 2011). Total RNA extracted from control and submerged tissue from three independent experiments consisting each of four individuals were used to construct cDNA indexed libraries and sequenced in a HiSeq2500 (Illumina) at 1x50 format, making a total of 12 sequenced libraries (tolerant and intolerant ecotype, control and submerged, all experimental triplicates) in a 2-lane format. RNA integrity, library construction and sequencing was performed as a service at the Unidad Universitaria de Secuenciacion Masiva, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico (IBT-UNAM). Differential Gene Expression (DGE) analysis was performed with edgeR using a generalized linear model and false discovery rate <0.05 (FDR). To group differentially expressed transcripts a logFC value of 1.5 (up-regulated) or -1.5 (down-regulated) and a FDR <0.05x10-5 were selected. GO analysis of differential transcripts was performed at phytozome.org Results: We identified commonly up-regulated genes (317) and exclusively up-regulated in Bd2-3 (466) or Bd21 (706). Regarding down-regulation, 330 transcripts were common, an exclusively 851 and 1026 for Bd2-3 and Bd21, respectively. GO analysis indicated that oxidative stress, pathogen responses and nitric oxide homeostasis were the most differential characteristics of tolerant ecotype Bd2-3. Conclusions: The use of triplicate RNAseq data of transcriptomes expressed in ecotypes with contrasting tolerance to submergence under long-day light regime, allowed us to identify common responsive routes such as SUSY, glycolysis, anaerobic routes (alanine, ethanol, lactate, GABA) and glyoxylate cycle. It also enabled us to discover integrated oxidative stress and NO homeostasis pathways that are differentially expressed in the tolerant ecotype. We expect that this information can be translated to agricultural relevant plants to increase our knowledge and biotechnological possibilities on plant submergence stress. Sequenced libraries (triplicates, HiSeq2500 Illumina, 1x50 format) of aerial tissue (control and 48h submergence stress) of Brachypodium distachyon Bd21 (sensitive) and Bd2-3 (tolerant).
2016-01-04 | E-GEOD-74222 | biostudies-arrayexpress
Project description: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
2023-07-27 | GSE229886 | GEO
Project description:In this study we treated Brachypodium distachyon roots with synthetic auxin, 2,4-D, to induce nodule-like structures (NLS) and performed RNA-seq to assess transcriptome changes during NLS formation.
2018-04-22 | GSE97940 | GEO
Project description:ABSTRACT: Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional 70 and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group 75 of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3M-bM-^@M-2 UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr- siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements 80 through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes. Analysis of smRNA populations in Brachypodium plants challenged by abiotic stresses: To profile the populations of smRNAs in the model monocot Brachypodium distachyon and examine their regulation in response to abiotic stresses, we conducted high-throughput sequencing of small RNAs from plants exposed to four different abiotic stress conditions, cold, heat (air), heat (water immersion), and salt, in the wild type Brachypodium cultivar Bd21. For our experiments we used information from the literature to select two time-points for stress durations, short and long, which differed for each stress: cold (6 and 24 hours), heat-air (1 and 3 hours), heat-water (1 and 3 hours), and salt (48 hours). We generated small RNA libraries for Illumina sequencing (GAII) from the leaves of Brachypodium plants subjected to stresses and selected smRNAs between 15 and 40 nt in length, which we mapped to the Brachypodium genome.
2015-01-20 | E-GEOD-55217 | biostudies-arrayexpress
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
2009-06-08 | GSE16177 | GEO
Project description: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.
2022-07-11 | GSE206682 | GEO
Project description: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.
2022-04-25 | GSE201294 | GEO
Project description:We used Brachypodium distachyon (BD21) as a model grass to gain insight into the affected host molecular pathways upon infection of Panicum Mosaic Virus (PMV) together with its satellite virus, Satellite Panicum Mosaic Virus (SPMV). Brachypodium plants at 2-3 leaf stage were either mock inoculated or inoculated with PMV and PMV+SPMV. Total RNA was isolated from shoot tissues of control and treated plants and was subjected to microarray analysis.
2012-11-09 | E-MEXP-3729 | biostudies-arrayexpress
Project description:Deep sequencing of Brachypodium distachyon small RNA from panicles (flowers) was done to analyze the genome-wide distribution patterns of 1) total small RNA reads and loci, 2) 21 and 24 nucleotide repeat-normalized reads and 3) 21 and 24 nucleotide phased siRNA clusters relative to gene and transposable element density.
2010-02-15 | GSE20195 | GEO