ABSTRACT: blanc-08-01_2012_01_rnapaths_03 - rnapaths--3_02/2012 - Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT. - Identify transcripts that are significantly changed in double mutants (L1 vcs sgs2) (xrn4-5/sgs3-11) versus their respective single mutants (L1 vcs and L1 sgs2) (xrn4-5 and sgs3-11) , and identify transcripts that are changed among the single and double mutants compared to WT (Col) reference or to mutant L1 reference. 20 dye-swap - genotype comparaison
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:rs09-06_silencing-muntants - silencing mutants - Find endogenous targets of SDE3, SDE5 and IR71. - Lines IR71 KO n°3, smd8#25, sde3 (Col-0), sde5 (Col-0), Suc-SUL(Col-0) and Col-0 were grown for 11 days on MS solid medium, seedlings were then transferred in MS liquid medium and harvested 2.5 days after. Keywords: genotype comparaison 8 dye-swap - CATMA arrays
Project description:au09-03_gamma-irradiation - 2 doses of ionising radiations (x-rays) - Metabolic pathways involved in the response of plants to ionising radiation treatment. - Arabidopsis thaliana (Col-0) seeds were grown in Petri dishes under sterile conditions until they had 2-rosette-leaves (on average 10 days). Then they received a dose of 10 or 40 gray of X-ray (Faxitron HP). Plant were harvested 2 and 26 hours after irradiation, immediatly frozen and stored at -80°C until RNA extraction (Rneasy plant mini Kit, Qiagen) . Experiment was carried in duplicates and a non irradiated control was done for each time. 8 dye-swap - dose response,time course
Project description:au10-09_gemsupv2ts-7 - gemsupv2ts-7 - Determine the level of expression in transgenic plants expressing geminiviral gene silencing suppressors. - One transgenic line of Arabidopsis overexpressing the geminiviral silencing suppressor V2TS was grown in adition to a control and their total RNA was extracted in order to study its genetic expression profile. 3 dye-swap - gene knock in (transgenic)
Project description: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: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:cea11-02_phosphatin - transcriptomic analysis of phosphatin effect - Identification of transcriptomic modifications promoted by phosphatin (AC6) (a molecule mimicking Pi addition effects on Pi starved plants). - 40 µM Phosphatin was added to MS (diluted 10 times) containing 20µM phosphate medium and controls were grown on MS (diluted 10 times) containing 20µM phosphate or supplemented with 500 µM of Pi. For each ARN extraction their was 3 plates containing each 10 seedlings grown 13 days in vertical petri dishes. 6 dye-swap - treated vs untreated comparison
Project description:rs10-05_tcv - gene profiling of turnip crinkle virus (tcv) sirna - 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process? - This is a plant evolution project on TCV in which, the biological questions are: 1. What are the genes (including miRNA precursors) that are differentially regulated in Col0 and dcl234 mutant in wt conditions? 2. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in Col0 and dcl234 mutant? 3. There are also differentially regulated between the plant generations 1 (G1) and 11 (G11)? 4. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA after fitness experiment? 24 dye-swap - gene knock out,treated vs untreated comparison
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,M-bM-^@M-&), 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: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