Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis leaves and flowers labeled with three different kits and hybridized to AGRONOMICS1 arrays

ABSTRACT: RNA was labeled as technical replicates with three different kits and hybridized to AGRONOMICS1 arrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Lars Hennig

PROVIDER: E-TABM-870 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.

Rehrauer Hubert H Aquino Catharine C Gruissem Wilhelm W Henz Stefan R SR Hilson Pierre P Laubinger Sascha S Naouar Naira N Patrignani Andrea A Rombauts Stephane S Shu Huan H Van de Peer Yves Y Vuylsteke Marnik M Weigel Detlef D Zeller Georg G Hennig Lars L

Plant physiology 20091223 2

Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strand ...[more]

PMID: 20032078

Similar Datasets

Project description:Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment. Experiment Overall Design: Two individual biologica replicates, each containing material of five mature plants of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, respectively, were used for the microarray analysis. Plants were germinated on soil and kept under continuous light until the beginning of bolting and then transferred to the dark for 8 h. Dark-incubated mature plants were reilluminated for 30 min and subsequently harvested for RNA extraction. Experiment Overall Design: The EX1 (At4g33630) T-DNA insertion line SALK 002088 and EX2 (At1g27510) T-DNA insertion line SALK 012127 were obtained from the European Arabidopsis Stock Centre (NASC). Homozygous mutant lines were identified by PCR analysis by using T-DNA-, EX1- and EX2-specific primers. Both T-DNA-lines were crossed with a flu Col-0 line that had been obtained by 5 backcrosses of flu1-1 in Landsberg erecta with wild-type Columbia. The ex1/flu and ex2/flu mutant lines were crossed, and within the segregating F2 population triple mutants were identified by PCR-based genotyping. For the cultivation of mature plants, seeds of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, all in Col-0 ecotype, were sown on soil and plants were grown under continuous light (100 mol m 2 s 1).

Dataset Information

Transcription profiling of Arabidopsis leaves and flowers labeled with three different kits and hybridized to AGRONOMICS1 arrays

Publications

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets