Rosette iron deficiency transcript profiling in Arabidopsis thaliana ecotypes Kas-1 and Tsu-1
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE39268 | GEO | 2012/09/30
SECONDARY ACCESSION(S): PRJNA170439
REPOSITORIES: GEO
Similar Datasets
Project description:Iron (Fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils. Under Fe deficiency, plant responses include upregulation of genes involved in Fe uptake from the soil. However, little is known about shoot responses to Fe deficiency. Using microarrays to probe gene expression in Kas-1 and Tsu-1 ecotypes of Arabidopsis thaliana revealed conserved rosette gene expression responses to Fe deficiency. Fe regulated genes included known metal homeostasis-related genes, and a number of genes of unknown function. Kas and Tsu Arabidopsis seedlings were grown on complete media for 24 d, and then put on complete or -Fe media and collected after 24 and 48 h.
2012-09-30 | E-GEOD-39268 | biostudies-arrayexpress
Project description:Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories. We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1).
2011-10-06 | GSE29086 | GEO
Project description:Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories. We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1). Arabidopsis thaliana roots from the Kas-1 and Tsu-1 ecotypes were exposed to complete or -Fe nutrient solutions and collected after 24 and 48 h for RNA extraction and hybridization on Affymetrix microarrays. Experiments were done using three biological replicates.
2011-10-05 | E-GEOD-29086 | biostudies-arrayexpress
Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.
2010-02-17 | GSE20340 | GEO
Project description:These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes â i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content. Microarray transcript profiling of leaf RNA identified a large number (5,996) of genes exhibiting robust constitutive differences in expression including many genes involved in general growth and development as well as abiotic stress pathways. Interestingly, mild soil drying resulted in only subtle physiological responses but resulted in gene expression changes in hundreds of transcripts, including 352 genes exhibiting differential responses between accessions. Our results highlight the value of genomic studies of natural accessions as well as identify a number of candidate genes for the observed constitutive and induced physiological differences between Tsu-1 and Kas-1. The basic experimental design involves two accessions (Tsu-1 and Kas-1) crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination (2 x 2 x 6 =24 arrays total)
2010-02-16 | E-GEOD-20339 | biostudies-arrayexpress
Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes â i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content. Each accession has 6 replicates, single channel on the ATH1 array. Samples were processed in two balanced batches (bioprime random labeling, hybridization,scanning). A total of 18 arrays
2010-02-16 | E-GEOD-20340 | biostudies-arrayexpress
Project description:These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content. Microarray transcript profiling of leaf RNA identified a large number (5,996) of genes exhibiting robust constitutive differences in expression including many genes involved in general growth and development as well as abiotic stress pathways. Interestingly, mild soil drying resulted in only subtle physiological responses but resulted in gene expression changes in hundreds of transcripts, including 352 genes exhibiting differential responses between accessions. Our results highlight the value of genomic studies of natural accessions as well as identify a number of candidate genes for the observed constitutive and induced physiological differences between Tsu-1 and Kas-1.
2010-02-17 | GSE20339 | GEO
Project description:Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source, and specific bioinformatic analyzer for KAS-seq data are still lacking. Here we present KAS-Analyzer as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-Analyzer can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-Analyzer introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-Analyzer provides a powerful framework to study transient transcriptional regulatory programs. KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.
2022-07-27 | GSE202044 | GEO
Project description:Progeny from a cross of Arabidopsis thaliana Landsberg (Ler, Poland) and Kashmir-2 (Kas-2, central Asia) accessions exhibit immune-related hybrid incompatibility (HI) due to a genetic interaction between a cluster of eight TNL (Toll/Interleukin1 Receptor- Nucleotide Binding - Leucine Rich Repeat) RPP1-like (Recognition of Peronospora parasitica 1-like) genes (R1- R8) from Ler and central Asian alleles of a Strubbelig-family receptor-like kinase (SRF3). In characterizing mutants altered in Ler/Kas-2 HI, we mapped multiple intragenic mutations to the RPP1-like Ler locus. The expression of sulki1 (suppressor of Ler/Kas-2 incompatibility 1) mutant mapping to RPP1-like R8 Ler, the parental line Kas-2 accession and the Ler/Kas-2 NIL have been determined by RNA-seq in 5-week old plants grown at 14 - 16 ºC.
2018-05-16 | E-MTAB-6755 | biostudies-arrayexpress
Project description:Iron (Fe) and copper (Cu) are essential metal micronutrients that are necessary for many redox reactions. The uptake of these metals is tightly regulated in plants. Some redox processes can alternatively use Fe-containing proteins or Cu-containing proteins, depending on nutritional status. Copper deficiency can rescue a Cucumis melo Fe uptake deficient mutant, and Fe deficiency can result in increased accumulation of Cu. However, the system responsible for Fe-deficiency-regulated Cu-uptake is unknown. To understand the genes and gene networks associated with Fe-deficiency regulated Cu uptake and Fe-Cu cross-talk, we conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions.
2018-03-01 | GSE104916 | GEO