Project description:rs09-03_zf1 - zf1 experiment - Transcriptome analysis of mutants for novel AGO-hook type proteins in Arabidopsis thaliana - 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
Project description:Conventional preparation methods of plant ribosomes fail to resolve non-translating chloroplast or cytoplasmic ribosome subunits from translating fractions. We established preparation of these ribosome complexes from Arabidopsis thaliana leaf, root, and seed tissues by optimized sucrose density gradient centrifugation of protease protected plant extracts. The method co-purified non-translating 30S and 40S ribosome subunits, separated non-translating 50S from 60S subunits, and resolved assembled monosomes from low oligomeric polysomes. Combining ribosome fractionation with microfluidic rRNA analysis and proteomics, we characterized the rRNA and ribosomal protein (RP) composition. The identity of cytoplasmic and chloroplast ribosome complexes and the presence of ribosome biogenesis factors in the 60S - 80S sedimentation interval were verified. In vivo cross-linking of leaf tissue stabilized ribosome biogenesis complexes but induced polysome run-off. Omitting cross-linking, the established paired fractionation and proteome analysis monitored relative abundances of plant chloroplast and cytoplasmic ribosome fractions and enabled analysis of RP composition and ribosome associated proteins including transiently associated biogenesis factors.
Project description:rs09-03_zf1 - zf1 experiment - Transcriptome analysis of mutants for novel AGO-hook type proteins in Arabidopsis thaliana - 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 4 dye-swap - CATMA arrays
Project description:Here we profiled small RNAs from whole cell, cytoplasmic and nuclear extracts from three-week-old Arabidopsis seedlings. We unexpectedly found that nuclear functional hc-siRNAs are predominantly present in the cytoplasm. Samples from Arabidopsis thaliana whole cell, cytoplasmic and nuclear extracts with 3 replicates for each. 9 samples in all.
Project description:Natural variation of secondary metabolism between different accessions of Arabidopsis thaliana has been studied extensively. In this study, we extended the natural variation approach by including biological variability and analyzed root metabolic patterns as well as their variability between plants and naturally occurring accessions. <p/> To screen 19 accessions of A. thaliana, comprehensive non-targeted metabolite profiling of single plant root extracts was performed using UPLC/ESI-QTOF-MS and GC/EI-QMS. 98 (GC/MS) and 139 (LC/MS) metabolites were identified at MSI levels one or two, or characterised ad level three. <p/> All metabolic profiles indicated that plant-to-plant-variability is greater than natural variation between accessions and non-biological variation of experimental batches. Ratios of plant-to-plant to total variability were high and distinct for the classes of known secondary metabolites, which are commonly subjected to natural variation analysis. None of the investigated accessions displayed a specifically high or low biological variability for these substance classes.
Project description:m6A profiling in two accessions of Arabidopsis thaliana (Can-0 and Hen-16) using the m6A-targeted antibody coupled with high-throughput sequencing