Illumina RNA-Seq for the barley pan-transcriptome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB64639 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Iso-Seq for the barley pan-transcriptome
| PRJEB64637 | ENA
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the peduncle tissue samples.
2023-08-21 | E-MTAB-13232 | biostudies-arrayexpress
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the inflorescence tissue samples.
2023-08-21 | E-MTAB-13233 | biostudies-arrayexpress
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the root tissue samples.
2023-08-21 | E-MTAB-13235 | biostudies-arrayexpress
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the crown tissue samples.
2023-08-21 | E-MTAB-13234 | biostudies-arrayexpress
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the grain tissue samples.
2023-08-21 | E-MTAB-13236 | biostudies-arrayexpress
Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the spikelet tissue samples.
2023-08-22 | E-MTAB-13231 | biostudies-arrayexpress
Project description:Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform.We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and "target-based" contig clustering. We then selected a conservative set of 15,527 contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in RNA-seq based measurements of gene expression.We developed a pipeline that makes de novo transcriptome sequencing possible in virtually any organism at a very reasonable cost ($6,300 in sequencing costs in our case). We anticipate that our approach could be used to develop genomic resources in a diversity of systems for which full genome sequence is currently unavailable. Our An. funestus contig set and analytical results provide a valuable resource for future studies in this non-model, but epidemiologically critical, vector insect.
| S-EPMC2996306 | biostudies-literature
Project description:Illumina sequencing of RNA from 14 wild barley samples (Hordeum spontaneum)
| PRJEB4947 | ENA
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