Arabidopsis thaliana ecotype Col-0 versus T-DNA mutant sir1-1
ABSTRACT: Arabidopsis thaliana Col-0 plants were compared to sir1-1 T-DNA insertion mutants to investigate transcript levels of sulfur metabolism related genes under standard conditions. Overall design: For wildtype Col-0 and sir1-1, leaf tissue was harvested from 3 independent plants that were 7 weeks old; total RNA was extracted, reverse transcribed and labeled with Cy3 or Cy5, hybridised on custom made array.
INSTRUMENT(S): University of Heidelberg custom made sulfur 5.4K array
Project description:Arabidopsis thaliana Col-0 plants were compared to sir1-1 T-DNA insertion mutants to investigate transcript levels of sulfur metabolism related genes under standard conditions. For wildtype Col-0 and sir1-1, leaf tissue was harvested from 3 independent plants that were 7 weeks old; total RNA was extracted, reverse transcribed and labeled with Cy3 or Cy5, hybridised on custom made array.
Project description:Technical replicates hybridisations using 1.04 Arabidopsis thaliana - columbia-0 plants :plants cultivated and RNA-extracted by VIB, amplified and hybridised at URGV. aVIB-Col_vs_aVIB-Col
Project description:In this experiment we investigate the transcription profile of M. inocognita infection at the start of the infection and 7 days later in A. thalinana Col-0 plants. This was compared to M. incognita infected material of the plant line erf6-1, a T-DNA insertion mutant in ERF6. The data showed the role of ERF6 during early M. incognita infection in Arabidaaaaaaaaaaopsis besides more insight in the transcription regulated by M. incognita in Col-0 the wildtype plant. Samples are taken from whole root systems of 14 (0 days after infection) or 21 (7 days after infection) day old plants.
Project description:Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone, including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing. Overall design: The near isogenic line Col-S and its parents Col-0 and Cvi-0 were grown for three weeks and treated with 350 ppb ozone for two hours. The whole rosettas were harvested from controls and and ozone treated plants. Three separate biological repeats used for RNA-seq analysis.
Project description:Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is the first layer of molecular defense encountered by pathogens when they attempt to infect plants. MTI is dependent on cell surface pattern-recognition receptors (PRR) which act upstream of mitogen-activated protein kinase (MAPK) pathways. Genetic screening and mutant knock-out lines have largely contributed to our knowledge of MTI. However, genetic screening is confined to phenotype-causing mutations and scarcely enables the discovery of redundantly-acting proteins. We sought to discover protein components that contribute in MTI, using a phenotype-independent approach to discern nucleus-localized proteins after MTI induction. We report on the nuclear proteome of Columbia-0 (Col-0) and chitin elicitor receptor kinase 1 (cerk1) mutant plants 15 min after MTI induction. Our approach revealed that MAMP-treated cerk1 plants had many proteins in common with Col-0-treated plants following chitosan treatment. cerk1 plants also manifested several unique proteins that were absent from Col-0 plants when elicited with chitosan indicating that they also perceive chitosan. Detailed analysis of the identified proteins revealed a nuclear accumulation of transcriptional regulators and transcription factors, DNA-modifying enzymes, RNA-binding proteins and ribosomal proteins. No novel MAPKs were found although Receptor for activated C kinase 1, a scaffold protein involved in defense, and a nucleotide binding leucine-rich repeat protein, implicated in resistance to Leptosphaeria maculans, were discovered in the nucleus of chitosan-treated plants and absent from water-treated control plants.
Project description:A dye swap experiment to compare Arabidopsis thaliana ecotype Col-0 with Arabidopsis thaliana ecotype Ler, both grown to Boyes scale 1.04 at VIB, Plant systems biology, Gent, Belgium
Project description:Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 inflorescences Overall design: mRNA profil of Arabidopsis Col-0 WT inflorescences were generated by paired-end deep sequencing, in replicate using Illumina HiSeq 2000
Project description:Changes in histone H4 acetylation of Arabidopsis thaliana (Col-0) by treatment with acetic acid. Overall design: 2weeks-old wild-type plants of A.thaliana (Col-0) were treated with/without 10mM aetic acid for 9days.
Project description:Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 siliques. Overall design: mRNA profiles of Arabidopsis Col-0 WT siliques were generated by paired-end deep sequencing, in replicate using Illumina HiSeq 2000.