E-GEOD-55482
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-55482 | ExpressionAtlas | 2015-12-02
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-55482-analysis-methods.tsv | Tabular | |||
| E-GEOD-55482-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-55482-coexpressions.tsv.gz | Tabular | |||
| E-GEOD-55482-configuration.xml | Xml | |||
| E-GEOD-55482-factors.xml | Xml |
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Similar Datasets
Project description:We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provides a resource to assess allele-specific gene expression between A. thaliana accessions.
2014-03-01 | GSE55482 | GEO
Project description:Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource
| PRJNA239720 | ENA
Project description:We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provides a resource to assess allele-specific gene expression between A. thaliana accessions. With 18 of the MAGIC parental inbred accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) crosses were performed to generate 9 sets of F1 progeny from which RNA was extracted with biological replication (three replicates) and for which mRNA-seq was performed to generate strand-specific reads. Library construction and sequencing was performed such that each set of biological replicates were sequenced as a pool (with 9-plex barcoding; each 9-plex was run on two HiSeq lanes).
2014-03-01 | E-GEOD-55482 | biostudies-arrayexpress
Project description:In this study, we describe the impact of genetic variation on transcript abundance in an F2 population of Arabidopsis thaliana. The RNA-seq resource generated by this study is suitable for expression quantitative trait locus (eQTL) mapping. From the aligned RNA-seq reads, and available genomic data for each of the parents of the cross, we imputed the genomes of each F2 individual (to allow genetic mapping of RNA abundance traits; briefly, genetic differences in aligned RNA-seq reads were used to impute each F2 genome). Our results show that heritable differences on gene expression can be detected using F2 populations (that is, single F2 plants), and shed light on the control of expression differences among strains of this reference plant.
2017-03-15 | GSE92568 | GEO
Project description:Hybridization of diverged taxa often result in lethality or sterility. We previously described natural variation for postzygotic incompatibility in the cross of diploid Arabidopsis thaliana to Arabidopsis arenosa. Hybrid seed death in this system has a complex genetic basis, involving many non-additive interactions. While activation of AGAMOUS-LIKE genes (AGL) and Athila elements have been detected 5-8 days after pollination (DAP), the molecular basis of death remains mysterious. To address this problem, we compared 3DAP transcriptomes in interspecific hybrids from two A. thaliana ecotypes, one compatible, the other incompatible. Relative to self crosses of the respective A. thaliana seed parent, hybrids displayed differential expression of key developmental regulators in both the endosperm and maternal seed coat as well as natural variation for stress response genes. Ribosomal protein genes and a photosynthetic cluster of genes were hyperactivated, presumably in response to growth signals. Suppressing endosperm growth factor IKU1 and defense response regulators such as NON-EXPRESSOR OF PATHOGENESIS RELATED1 (NPR1) improved hybrid seed survival. Therefore, in incompatible hybrids disruption of seed development most likely initiates in the endosperm, rapidly affecting embryo and seed coat. The activation of putative POLYCOMB REPRESSIVE COMPLEX (PRC) gene targets, together with a twenty-fold reduction in expression of the FERTILIZATION INDEPENDENT SEED 2 gene, indicates a PRC role. Examination of differential gene expression of incompatible A. thaliana eco. Col-0 X A. arenosa and compatible A. thaliana eco. C24 X A. arenosa hybrid seeds plus corresponding A. thaliana and A. arenosa control crosses.
2013-06-05 | E-GEOD-42957 | biostudies-arrayexpress
Project description:Genomic DNA of Col, Van and reciprocal hybrids, bioprime random labeling, and hybridization to AtTILE1 forward array. Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.
2008-11-18 | GSE13620 | GEO
Project description:Hybrid vigor or heterosis has been widely applied in agriculture and extensively studied at the genetic and gene expression levels. However, the biochemical mechanism underlying heterosis remains elusive. One theory suggests that a decrease in protein aggregation may occur in hybrids due to the presence of protein variants between parental alleles, but it has not been experimentally tested. Here, we report comparative analysis of soluble and insoluble proteomes in Arabidopsis intraspecific and interspecific hybrids or allotetraploids formed between A. thaliana and A. arenosa. Both intraspecific hybrids and interspecific allotetraploids displayed non-additivity of the expressed proteins, including many biotic and abiotic stress-responsive proteins. In the allotetraploids, homoeolog-expression bias was not observed among all proteins examined but could occur among 17-20% of the nonadditively expressed proteins with more A. thaliana-biased than A. arenosa-biased homoeologs, consistent with the transcriptome results. Analysis of the insoluble and soluble proteomes revealed more soluble proteins in the hybrids than their parents but not in allotetraploids. Most proteins in ribosomal biosynthesis and in the thylakoid lumen, membrane, and stroma, were in the soluble fractions, indicating a role of protein stability in photosynthetic activities for promoting growth. Together, these results support roles for nonadditive expression of stress-responsive proteins and reduction of protein biosynthesis in mediating heterosis in Arabidopsis hybrids and allotetraploids.
2022-06-17 | MSV000089682 | MassIVE
Project description:We produced RNA-Seq reads from messenger RNA isolated from root tissue for the 19 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature 477:419-23 for a description of the MAGIC genetic mapping resource). The read data was generated with biological replication (two replicates). The resulting RNA-Seq data provide a resource to assess root gene expression across different accessions of A. thaliana. Comparable RNA-Seq read data for the MAGIC founder accessions for aerial seedling tissue has previously been released under GEO series GSE30720 (Gan et al. 2011. Nature, 477:419-23).
2013-12-11 | GSE53198 | GEO
Project description:We produced RNA-Seq reads from messenger RNA isolated from seedling, root, and floral bud tissue for 17 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provide a resource to assess tissue-specific expression across different accessions of A. thaliana. Note that comparable read data for accessions Col-0 and Can-0, which are also founders of the MAGIC lines, has previously been released under GEO series GSE30795 (Gan et al. 2011. Nature, 477:419-23).
2013-12-11 | GSE53197 | GEO
Project description:Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disrupts local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic risks posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of late sac fry of a European (EO) farmed (“StofnFiskur”, Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected fewer differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the fitness of wild populations.
2022-03-11 | GSE184425 | GEO