SOLiD sequencing of Noccaea (Thlaspi) caerulescens root transcriptomes from three contrasting ecotypes
Ontology highlight
ABSTRACT:
ORGANISM(S): Noccaea caerulescens
PROVIDER: GSE35900 | GEO | 2014/02/28
SECONDARY ACCESSION(S): PRJNA151997
REPOSITORIES: GEO
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2014-02-28 | E-GEOD-35900 | biostudies-arrayexpress
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2010-04-20 | GSE20223 | GEO
Project description:The plant hormone gibberellin (GA) represents an important regulator of growth and development. Early transcriptional events controlled by GA are not well characterised. Previous microarray studies have identified genes responsive to GA treatment in the whole seedling. The whole seedling represents many tissues where subtle effects of GA treatment in specific tissues may be masked. When treated with GA, an effect on the growth rate of roots was observed. More specifically, the shorter root of a GA-deficient plant can be rescued to wild-type length by the application of GA. This experiment was designed to identify GA-regulated genes in the root tips of Arabidopsis. The use of a GA-deficient mutant provides a greater potential to identify genes responding to GA treatment. Root tips are ideally suited for the quick uptake of the hormone treatment. There will be two biological replicates which will each consist of a control treatment at 0 minutes and 2 hours, as well as the experimental GA-treated 2 hour time point. This system provides an opportunity to compare gene expression between treated and non-treated root tips and allow the identification of early GA-responsive genes. 6 samples were used in this experiment.
2010-04-28 | E-GEOD-20223 | biostudies-arrayexpress
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2013-12-11 | GSE53198 | GEO
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Project description:Expression level polymorphisms (ELPs) often result in cis-acting expression quantitative trait loci (cis-eQTL), which are important QTL and association mapping tools and account significantly for phenotypic variability. Generally, it is assumed that such stably heritable ELP represent regulatory element polymorphisms in the respective genes. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here we analyzed heritability of ELP observed between Arabidopsis thaliana accessions Eil-0 and Lc-0 by comparing genotyped recombinant inbred lines (RIL) to their parents in microarray analyses. Keywords: expression level polymorphism, Arabidopsis thaliana accessions, recombinant inbred lines In order to analyze expression level polymorphisms between the accessions Eil-0 and Lc-0, three independently grown seedling pools were analyzed by two color co-hybridization of the labeled cDNAs in dyeswap experiments, giving a total of six slides. For the analysis of gene expression in seedlings of 7 different RILs, each RIL sample was co-hybridized with each parent (Eil-0 and Lc-0) in a dyeswap, resulting in two slides per parent vs. RIL comparison. The total number of slides in this study was 34.
2010-05-16 | E-GEOD-13628 | biostudies-arrayexpress
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
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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). Examination of RNA expression in root for the 19 Arabidopsis thaliana accessions used as parents for the MAGIC lines (parental accessions are Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, Zu-0).
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