Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis CAF-1 depletion/gamma-irradiation

ABSTRACT: CAF-1 is involved in nucleosome assembly following DNA replication and nucleotide excision repair. In Arabidopsis thaliana, the 3 CAF-1 subunits p150, p60 and p48 are encoded by FAS1, FAS2 and, most likely, MSI1, respectively.fas mutants exhibited increased levels of DNA double-strand breaks, a G2 phase retardation, and elevated levels of mRNAs coding for proteins involved in homologous recombinational repair. The same genes that were transcriptionally up-regulated in the fas mutants were also found to have a higher steady state level of transcription in wild-type Arabidopsis plants exposed to gamma-irradiation. Experiment Overall Design: Total RNA prepared from 4-week-old seedlings (without the roots i.e. true leaves with cotyledon and hypocotyls) using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Four-week-old sterile seedlings of wild-type plants (ecotype Nossen) were irradiated with 100 Gy of gamma-rays at a dose rate of 300 Gy/h. Six and 12 hours after irradiation, samples were frozen in liquid nitrogen and immediately ground for total RNA isolation. After confirming its quality, extracted RNA was prepared for microarray analysis. An Arabidopsis 2 Oligo Microarray kit (Agilent Technology, CA, USA) was used in this study. After confirming its quality, extracted RNA was prepared for microarray analysis as described by the manufacturer (Agilent) using the suggested chemicals and reagents.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Masaki Endo

PROVIDER: E-GEOD-5043 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:RNA from the aerial parts of 15-day-old eceriferum cer6-2 mutant and control plants were used in microarray experiments to screen for differentially expressed genes. Among those which were down regulated in the mutant, several were known to be involved in various plant defense mechanisms. The most remarkable difference was measured for the transcripts encoding the pathogenesis-related protein1 (PR-1), which is a marker of the systemic acquired resistance (SAR) pathway, with a 100-fold decrease in the cer6-2 mutant. Further Q-PCR experiments showed that the PR-1 transcript levels were low in two other eceriferum mutants, representing 1/200th and 1/25th of the normal values in the aerial part of 15-day-old cer2 and cer1-1 mutants, respectively. Interestingly, PR-1 mRNA levels were closed to the normal values in the cer3-1 and cer6-2R mutant, the latter being a plant where the synthesis of the very-long chain fatty acids, which is deficient in the cer6-2 plants, is partially restored. Altogether, these results strongly suggested that the amount of PR1-mRNA was not directly correlated to the amount of epicuticular wax on the leaves, but was rather correlated to the presence or absence of some particular lipid-constituents in the epicuticular wax layer. Related publication:; Garbay B, Tautu MT, Costaglioli P. Low level of pathogenesis-related protein 1 mRNA expression in 15-day-old Arabidopsis cer6-2 and cer2 eceriferum mutants. Plant Science 2007; Volume 172, Issue 2, Pages 299-305 Experiment Overall Design: Total RNA was purified from the aerial parts of 2-week-old plants (20 plants were pooled for each genotype). Arabidopsis plants were grown under long-day conditions (16 h light:8 h dark) at 22Â°C and 80% relative humidity. The control plants and the cer mutant were cultivated in the same phytotron, and the Petri dishes were placed randomly on the same shelf. This was done to avoid any difference in plant growth conditions between the mutants and the control plants. The microarrays used were Agilent Arabidopsis2. GSM87735 represents the direct experiment (cer6-2 Cy3, Ler-0 Cy5), and GSM88340 represents the dye-swap (Ler-0 Cy3, cer6-2 Cy5)

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Transcription profiling of Arabidopsis CAF-1 depletion/gamma-irradiation

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