Endogenous hairpins-ir71 targets : Gene profiling of Turnip Crinkle Virus (TCV) siRNA in mutants.
ABSTRACT: gnp06-03_microtrac Endogenous hairpins-ir71 targets What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants? Lines IR71 KO n°3 and Col-0 were grown on soil until bolting, Flower buds were then harvested and RNA extracted with Qiagen RNeasy Plant mini kit. RNA was stored at -20°C. 3 dye-swap - gene knock out
Project description:ra11-04_qtl - study of the transcriptional consequences of a growth qtl candidate (sg1) - We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level. - We are analysing a QTL named Sg1 quantitatively affecting the shoot growth in Arabidopsis thaliana. Sg1 mutation exhibits a large set of phenotypic consequences (growth, fitness,…), and the penetrance of these defects increase over generations. The CATMA collaboration aims to perform a T-DNA mutant vs WT analysis, with the WT control being derived from the heterozygous T-DNA parent. A first homozygous generation hypotheticaly derived from the heterozygous T-DNA parent and a 4th homozygous generation showing more severe phenotypes are being compared to the WT (dye swap, biological repetitions). Whole plants were harvested 10 DAG at 11am for each genotype. 4 dye-swap - gene knock out
Project description:rs09-10_fwa - wt vs mutants 09. Impact of loss of DNA methylation and small interference RNAs (siRNAs) in gene expression. Determination of the genes misregulated upon ectopic expression of the FWA imprinted gene. Mutants impaired for the DNA methylation maintenance pathway and RNA interference machinery were compared to mutants simultaneously impaired for both. Impact of FWA and SDC ectopic expression. 15 dye-swaps. fwa-d, gain of function epimutation, gene knock-in (transgenic), gene knockout.
Project description:adt05-04_drn - drn/drn-l expressing cells vs non-expressing cells - DRN targets - In primordia timing (pt) mutant background DRN::erGFP transgenic cell culture (somatic embryos suitable to regenerate plants) has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells. Total RNA was extracted and sent to Evry for comparison (samples DRN a,b,c). DRN-L::erGFP transgenic cell culture has been protoplasted and protoplasts have been sorted for GFP+ and GFP- cells (samples DRN-L-2-1 and DRN-L-3-1). Keywords: null 5 dye-swap - CATMA arrays
Project description:ra10-04_roots - ws vs clca2/35a2/352.7 - What are the transcriptional adaptations induced by genetically modifying vacuolar nitrate transport - Plants were grown for 12 days after germination in vertical Petri dishes onto a 2mM NO3 medium (derived from Armengaud et al 2004) in long days (16h light at 65 µE). Samples consisted of pooled roots from at least 30 to 50 plants per sample. The experiment has been repeated 4 times (exp IFX1-IFX3-CPLA2-CPLA3)and samples were harvested around 11h in the morning (ie 3h after illumation). 10 dye-swap - gene knock out, genotype comparison, normal vs transgenic comparison
Project description:ra09-01_qtlleafgrowth - sg1-sg3 - What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level - Plants were grown in the in vitro conditions where we have mapped and cloned the concerned QTL and which allows us to see the phenotype linked to the segregation of the natural alleles. We are comparing 2 genotypes descending from a RIL from the Bur x Col RIL set, homozygous and identical everywhere in the genome except for the 23.4 kb at SG1 loci where one genotype is Bur (97.4 and 175.4) and the other is Col (97.1 and 175.1). 4 dye-swap - genotype comparison
Project description:gnp_blan06_torpten - rnai tor time course - The impact of the TOR pathway on growth and stress responses. Modification of translational and transcriptional profiles in Tor-inducible RNAi mutants and identification of TOR targets. 28 dye-swaps - normal vs. rnai mutant comparison.
Project description:rs11-09_meotic - time course expression profile of ap1-cal after induction of an ap1-transgene - CDKs are major regulators of the mitotic as well as the meiotic cell cycle. In comparison with the mitotic cell cycle much less is known about the regulation of meiosis, especially in plants. One of the reasons for this is the very low abundance and the difficult accessibility of cell undergoing meiosis. We have developed a system to enrich for meiocytes. This will be the material with which we will search for CDK substrates in a biochemical approach. To first get an overview about the meiotic genes expressed in this system, we want to perform here a time series at four time points after the induction that leads to the synchronized development of meiocytes. The in the microarray identified genes, will then set the frame for the upcoming biochemical experiments. - An ap1-cal double mutants carrying an Glucocorticoid-receptor fusion to AP1 was indcued and samples were collected 2 days after induction (dai), 8dapi, 9dai, 10dai and 11dai. Then, the expression profile of 2dai were compared with 8dai, 8 with 9, 9 with 10, and 10 with 11. 12 dye-swap - time course
Project description:rs10-01_rrm - quadruple rrm experience - What is the role of the RRM protein family in plants? Plants were grown on soil in controlled environment under LD (16 h light/8 h dark) and the rosette leaves (8-leaf stage seedlings) were collected for RNA preparation. Keywords: normal vs transgenic comparison 2 dye-swap - CATMA arrays
Project description:adt10-01_wip2 - wip overexpressing plants - Identification of genes induced or repressed by WIP genes - The objective is to identify genes responsible for the phenotypes observed in WIP overexpressing lines. WIP transcription factors are involved in reproductive and vegetative development by acting on the remodeling of various tissues. The WIP related processes have a major impact, in particular on reproduction (sex determination, fertilization, development of the seed). The way of action of these transcription factors is probably conserved, their effect depending only on their specificity of expression. Two WIP genes, NTT and TT1, was overexpressed in Arabidopsis thaliana. The objective is to compare the common deregulated genes (and in particular repressed) in the transcriptome of these two overexpressor lines, to highlight their mode of action and the way they act on the tissue in which they are expressed. Keywords: gene knock in (transgenic),normal vs transgenic comparaison 6 dye-swap - CATMA arrays