Expression data from torpedo-stage embryos from different Arabidopsis accessions
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ABSTRACT: The zll/ago10 mutant from Arabidopsis shows different expressivity of shoot stem cell defects in different Arabidopsis accessions. We used microarrays to identify changes in embryo gene expression associated with differences in zll expressivity. Microarrays from ZLL-dependent (Ler-1, Fe-1, Bay-0 and Nw-0) and ZLL-independent (Col-0, Van-0, Ts-1) accessions were compared (always using a minimum of 3 arrays in each group) in different combinations to identify differentially expressed genes.
Project description:STO2 is a novel MYB like protein which belongs to one of the most important transcription factors in planta. Microarray analysis of sto2 null mutant compared to Columbia with three-week-old soil-grown plants revealed that STO2 function in ABA and salt stress response. To find the potantial downstream target of STO2 protein, microarray was performed and samples from expanding rosette leaves (from 3th to 6th leaves) of three-week-old soil-grown sto2 mutant plants with those of wild-type were collected. Both Wild-type (Col-0) and sto2 null mutant have three biological replicates, respectively.
Project description:Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed. In order to identify potential direct/early target genes of EBE transcription factor, estradiol inducible overexpression system was used. Three week old Arabidopsis EBE-XVE (line 14) and WT seedlings were treated with ß-estradiol (2µM) for 45 min. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in 3 biological replications and genes differentially expressed between estradiol treated EBE-XVE and WT plants were identified as potential early targets of EBE.
Project description:Methylation state of human post-mortem brain tissue from the frontal lobe of patients with Frontotemporal Dementia caused by mutations in GRN, MAPT and C9orf72 and healthy controls
Project description:The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and the metabolic syndrome. This study aimed to identify genetic variants associated with liver weight, liver triglycerides, and body weight using the obese BFMI sub-line BFMI861-S1. BFMI861-S1 mice are insulin resistant and store ectopic fat in the liver.
Project description:Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts To identify genes more rapidly responding to elevated ORE1 expression we here repeated the previous experiment (Balazadeh et al., 2010), but shortened the EST induction time to 2 h (ORE1-IOE-2h dataset). Furthermore, to exclude potential misinterpretation due to EST treatment we also included an experiment where we transiently expressed a 35S::ORE1 construct in Arabidopsis mesophyll cell protoplasts and extracted RNA 6 h after the transfection (35S::ORE1-6h dataset);
Project description:Transcriptional profiling of A. thaliana seedlings (early development) at 7 time points We investigate biomass heterosis by scoring partial correlations of transcriptional profiles. We compare 4 genotypes: Col-0 (homozygous parental line), C24 (homozygous parental line), Col-0xC24 and C24xCol-0 (crossings) using 2-4 replicates each
Project description:Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using M-bM-^@M-^Xomics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes. Arabidopsis seedlings were grown in 30 mL of sterile liquid full nutrition (FN) medium (3 mM sulphate) or 150 M-NM-<M sulphate medium. Transferring pre-grown 7-days old seedlings to a sulphate depleted medium (0 M-NM-<M sulphate) assured immediate and continued sulphate starvation during the next two days of plant cultivation. On day 9 subsets of the sulphate depleted cultures were supplied with sulphate (500 M-NM-<M) and samples taken 30 min and 3 hours after re-supply. Four time points (full nutrition (FN), plants starved for 48 h (-S), plants re-supplied with sulphate for 30 minutes (30M-bM-^@M-^Y S) and plants re-supplied with sulphate for 3 hours (3 h S)) were subjected to the microarray analysis. Two biological repetitions of each sample were analyzed.
Project description:Calyx of Held giant presynaptic terminals in the medial nucleus of the trapezoid body of the auditory brainstem form axosomatic synapses that have advanced to one of the best-studied synaptic system of the mammalian brain. As the auditory system matures and adjusts to high fidelity synaptic transmission, the calyx undergoes extensive structural and functional changes: it is formed around postnatal day 3 (P3), achieves immature function until hearing onset around P10 and can be considered mature from P21 onwards. This setting provides the unique opportunity to examine the repertoire of genes driving synaptic structure and function. We performed cell type-specific gene expression profiling of globular bushy cells (GBCs), the neurons giving rise to the calyx of Held, at different maturational stages (P3, P8 and P21). We identified GBCs by stereotaxic injection of fluorescently labelled retrograde tracer Cholera toxin B into the contralateral MNTB of anesthetized rats. Animals were sacrificed 24h after injection, the brain was taken out and flash frozen. 12um thick brainstem cryosections were prepared and 200 fluorescently labelled GBCs per animal were excised from the VCN using laser microdissection. Cells were collected from 6 animals at P3 (synapse formation), 9 animals at P8 (juvenile synapse) and 5 animals at P21 (mature synapse). RNA was isolated from the collected cells and linearly amplified in order to perform cell-type specific expression profiling.
Project description:To understand how an inhibition of the mitochondrial ATP synthase affects transcriptional programming and to identify potential candidates of the signaling machinery involved in ATP synthase deficiency responses, we used oligomycin on seedling liquid cultures. Seedlings were harvested at time points 0, 1 and 4 h after the start of oligomycin and control (EtOH) treatments. Already 1 h after addition of oligomycin a total of 102 genes were more than threefold up-regulated and 14 genes were repressed, with most of them showing persistent changes. After 4 h, 580 additional genes were more than threefold up-regulated, and 152 genes were repressed by oligomycin. Several genes for alternative NAD(P)H dehydrogenases and alternative oxidases (AOX1a, AOX1d and NDA1) were up-regulated early, and additional homologs (NDA2, NDB2, NDB4 and AOX1b) followed 4 h after the start of treatment. Several genes for subunits of complex I, complex IV and the ATP synthase were induced whereas hardly any genes encoding enzymes of glycolysis and the TCA cycle changed. Additionally, four of five hallmark genes for oxidative stress were increased by oligomycin. These genes are At2g21640 (UPOX), At1g19020, At1g05340 and At1g57630 and code for proteins of unknown function. Among oxidative stress proteins with known functions, several H2O2-responsive Glutathione-S-transferases and BCS1 (CYTOCHROME BC1 SYNTHESIS) were strongly up-regulated already after 1 h. BCS1 is induced by salicylic acid and independent of other reactive oxygen signaling (ROS) pathways, such as H2O2. The results indicate that several different ROS and defense signaling pathways were induced simultaneously by oligomycin. This is further corroborated by induction of several transcription factors of the WRKY and NAC families, which have been previously implicated in coordinating cellular defense signaling. Three replicates for each treatment including oligomycin and control (EtOH) samples.
Project description:gene expression profiling in different zones along the gradient of the growing maize leaf balde aover a time course of dirunal cycle and carbon starvation by extension of the night Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night, and in non-photosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades a defined developmental gradient facilitates analyses in the cell division, elongation and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn and 6, 14 and 24 hours into an extended night, and tracked whole leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose recovers partially between 14 and 24 h into the extended night in the growth zones but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in sucrose. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night and then partially recover indicating that growth processes are determined by local carbon status. The level of sucrose-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:sucrose ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones. 3 repliucates per time point and leaf region, each pooled form 5 indiviual plants