Hordeum vulgare isolate:highland barley
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ABSTRACT:
PROVIDER: PRJNA553630 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Highland barley Transcriptome
| PRJNA527673 | ENA
Project description:huless barley Raw sequence reads
| PRJNA675977 | ENA
Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.]
2011-11-22 | GSE33413 | GEO
Project description:We hypothesized that the genome segments of cultivated barley should show certain similarity with its ancestral wild barley. Instead of whole genome sequences, we employed RNA-Seq to investigated the genomic origin of modern cultivated barley using some representative wild barley genotypes from the Near East and Tibet, and representative world-wide selections of cultivated barley.
2014-10-06 | E-MTAB-4221 | biostudies-arrayexpress
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates. dRNA-seq analysis of total RNA from green and white plastids of the barley mutant line albostrians
2011-11-23 | E-GEOD-33773 | biostudies-arrayexpress
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
2011-11-23 | GSE33773 | GEO
Project description:Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding of the effect of waterlogging stress in barley, we carried out a genome-wide gene expression analysis in roots of Yerong and Deder2 barley genotypes under waterlogging and control (well-watered) conditions by RNA-Sequencing, using Illumina HiSeq™ 4000 platform.
2020-02-14 | GSE144077 | GEO
Project description:Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq.
2012-12-31 | E-MTAB-4428 | biostudies-arrayexpress
Project description:Senescence is the last developmental phase of plant tissues, plant organs and, in the case of monocarpic senescence, entire plants. In monocarpic crops such as barley, it leads to massive remobilization of nitrogen (primarily from degradation of photosynthetic proteins) and other nutrients to developing seeds. Senescence has therefore a major impact on both yield and seed/grain quality. To further investigate this process, a proteomic comparison of flag leaves of late-senescing barley variety ‘Karl’ and a near-isogenic early-senescing line, ‘10_11’, was performed at 14 and 21 days past anthesis, using both two-dimensional gel-based and label-free quantitative mass spectrometry-based (‘shotgun’) proteomic techniques. Overall, this approach identified >9,000 barley proteins, and one-third of them were quantified. Analysis focused on proteins that were significantly (P-value ≤0.05; difference ≥1.5-fold) upregulated in early-senescing line ‘10_11’ as compared to ‘Karl’, as these may be functionally important for the senescence process. Many proteins in this group, including several membrane and intracellular receptors, glucanases, enzymes with possible roles in cuticle modification, classical pathogenesis-related proteins, membrane transporters and proteins involved in DNA repair, have likely or putative functions in plant pathogen defense. Additionally, several proteases and elements of the ubiquitin-proteasome system were upregulated in line ‘10_11’; these proteins may be involved in nitrogen remobilization, and in the regulation of both senescence and plant defense reactions. Together, our data shed new light, at the protein level, on the importance of plant defense reactions during senescence, on senescence regulation, and possibly on crosstalk between senescence regulation and plant-pathogen interaction.
2017-02-08 | PXD002307 | Pride
Project description:Purpose: The goal of this study was to investigate the mechanisms involved in the initiation and development of crown-roots (CRs) in barley and to estimate the role of cytokinins (CKs) in this process. Method: stranded libraries were obtained from RNA extracted from the stem base of 1 day-after-germination (DAG) and 10DAG-seedlings of wild-type (WT) and AtCKX-overexpressing barley lines (OE-CKX). OE-CKX lines have a reduced content of endogenous CKs and are characterized by a higher number of CRs. Libraries were deep sequenced on Illumina HighSeq platform. Each sample was investigated in three independent biological replicates. Results: Using a data analysis workflow optimized for barley, we identified more than 4000 transcripts differentially expressed in the stem base of 1DAG and 10DAG-seedlings. Expression as determined by RNA-seq was validated by real-time PCR. Our data were compared to the transcriptomic profiling obtained from rice and we were able to identify genes potentially involved in the initiation/development of CRs in barley. Also the use of the transgenic line with altered endogenous CK content allowed us to conclude about the role of CKs in the process. Conclusions: Our study represents the first analysis aiming to understand the initiation and development of CRs in barley.
2016-11-01 | GSE87737 | GEO