B.napus sequencing
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR475359_1.fastq.gz | Fastqsanger.gz | |||
| ERR475359_2.fastq.gz | Fastqsanger.gz | |||
| ERR475360_1.fastq.gz | Fastqsanger.gz | |||
| ERR475360_2.fastq.gz | Fastqsanger.gz | |||
| ERR475361_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.
2009-05-03 | GSE15915 | GEO
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38018 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. microRNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38019 | biostudies-arrayexpress
Project description:Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulators are conserved in B. napus suggesting a shared regulatory network with other plants species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable, not only to evaluate germination performance of B. napus accessions, but also to identify key targets for crop improvement in this important process.
2019-09-11 | GSE137230 | GEO
Project description:Tissue-specific RNA profiling of the Brassica napus funiculus and funicular subcompartments using laser microdissection and RNA-sequencing
2015-08-20 | GSE71859 | GEO
Project description:ngs2017_08_brasilice-transilice - What are the genes with modulated expression in response to brassica napus treatment (1.7mM, One week, root supply)-Brassica napus were grown on hydropnic conditions using Hoagland nutrient solution containing or not 1.7 mM of Si
2019-02-22 | GSE122968 | GEO
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes. Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.
2010-05-19 | E-GEOD-15915 | biostudies-arrayexpress
Project description:mRNA expression profiling of the embryo, endosperm (micropylar, peripheral, chalazal), and seed coat (outer, inner, chalazal, chalazal proliferating tissue) of the developing Brassica napus seed. Tissues were isolated using laser microdissection (LMD) from Brassica napus seeds at the globular, heart, and mature green stages of seed development.
2024-07-15 | GSE271809 | GEO
Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray.
2013-03-01 | GSE43918 | GEO
Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray. The time course expression of 90K Brassica napus EST contigs were measured at 8 developing seed stages of 10, 15, 20, 25, 30, 35, 40 and 45 DAF (days after flowering) using single color microarray
2013-03-01 | E-GEOD-43918 | biostudies-arrayexpress