Expression data from torpedo-stage embryos from different Arabidopsis accessions
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE47884 | GEO | 2013/06/13
SECONDARY ACCESSION(S): PRJNA208237
REPOSITORIES: GEO
Similar Datasets
Project description:The zll/ago10 mutant from Arabidopsis shows different expressivity of shoot stem cell defects in different Arabidopsis accessions. We used microarrays to identify changes in embryo gene expression associated with differences in zll expressivity. Microarrays from ZLL-dependent (Ler-1, Fe-1, Bay-0 and Nw-0) and ZLL-independent (Col-0, Van-0, Ts-1) accessions were compared (always using a minimum of 3 arrays in each group) in different combinations to identify differentially expressed genes.
2013-06-13 | E-GEOD-47884 | biostudies-arrayexpress
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Background: Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomics strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis (BSA) and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Methodology/Principal Findings: Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that Ts-1 and Tsu-1 accumulate higher shoot levels of Na+ than Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence ~5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1-1 null mutant, under NaCl stress conditions this novel AtHKT1 allele not only does not confer NaCl sensitivity, but co-segregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; www.purdue.edu/dp/ionomics). Conclusions/Significance: Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the causal locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1, two coastal populations of Arabidopsis. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions, and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes. Keywords: genomics hybridization bulk segregant analysis
2006-11-18 | GSE6203 | GEO
Project description:The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression.
2012-08-04 | GSE39885 | GEO
Project description:Background:; Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomics strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis (BSA) and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Methodology/Principal Findings:; Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that Ts-1 and Tsu-1 accumulate higher shoot levels of Na+ than Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence ~5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1-1 null mutant, under NaCl stress conditions this novel AtHKT1 allele not only does not confer NaCl sensitivity, but co-segregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; www.purdue.edu/dp/ionomics). Conclusions/Significance:; Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the causal locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1, two coastal populations of Arabidopsis. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions, and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes. Experiment Overall Design: Hybridizations from two sets of Bulk Segregant analysis. F2 populations from col-0 crossed to two High Na accessions: Ts-1 and Tsu-1 were analyzed. This series contains the 3 hybs from each accession that were used to identify Single Feature Polymorphisms, the 3 hybs of Col-0 they were compared to, and 1 hyb for each pool from the BSA mapping(High Na pool, low Na Pool).
2008-06-14 | E-GEOD-6203 | biostudies-arrayexpress
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:The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression. Homozygous T2 progeny of complemented plants expressing ago10-3;PAGO10-HF-AGO10 and ago1;PAGO1-HF-AGO1 were used for preparation of AGO complexes. Flower samples including floral buds, open flowers, and newly set siliques (1-2 day old) were collected for protein extraction and isolation of dual-tagged AGO complexes using a two-step affinity purification. The isolated AGO complexes were divided into two parts, one aliquot was used for sRNA extraction with Trizol reagent, whereas the other part was used for monitoring protein purity by Gelcode blue staining and western blot using a monoclonal anti-Flag antibody (Sigma) as previous described.
2012-08-03 | E-GEOD-39885 | biostudies-arrayexpress
Project description:In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.
2017-05-21 | GSE94762 | GEO
Project description:We have sequenced messenger RNA isolated from seedling tissue for 19 accessions of Arabidopsis thaliana (with biological replication). The 19 accessions for which RNA-Seq reads were collected have served as the founders for the MAGIC lines, a high-resolution recombinant inbred line mapping resource. RNA sequencing data was used to examine differential gene expression among the accessions.
2011-08-29 | GSE30720 | GEO
Project description:a2e_heterosis - cgh_colvsc24_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24.
2011-05-17 | GSE24831 | GEO