Project description:Different fuctional genes have different expression levels in various tissues. Along with the seasons changing, expression level also changes. One-year expression level for functional genes can be indicated by the four seasonal samples and respective time-course change can also be detected. We use microarry chips to study the expression levels for specific genes and explore new functional genes involved in secondary metabolism Samples from four tissues (bud, root, xylem and phloem) were collected in different seasons in one year. April and May were the months in spring for collecting samples. June and July were the months in summer for collecting samples. September and October were the months in autumn for collecting samples. December was the month for collecting samples in winter. RNA from each sample was extracted for hybridization.

2014-03-20 | E-GEOD-56023 | biostudies-arrayexpress

Microarray analysis of Bay-0 x Sha recombinant inbred lines at four seed germination stages

Project description:Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we measured gene expression levels of Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using. We mapped the eQTL of the gene expression and the result displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.

2020-06-24 | E-MTAB-9080 | biostudies-arrayexpress

Mechanism and cellular actions of the potent AMPK inhibitor BAY-3827

Project description:Inhibition of AMP-activated protein kinase (AMPK) is increasingly being explored for its therapeutic potential in some diseases, including certain types of cancers. However, AMPK-inhibitory tool compounds have largely been limited to compound C/dorsomorphin and SBI-0206965, both of which display numerous off-target effects and blocking AMPK-independent metabolic processes. Here we describe molecular insights and cellular actions/utility of a recently identified potent AMPK inhibitor BAY-3827. Sequence analysis of highly/lowly-inhibited kinases by BAY-3827, based on in vitro kinase selectivity profiling, predicted key conserved residues involved in the compound-inhibitory effect. A co-crystal structure of the AMPK kinase domain (KD)-BAY-3827 complex resolved at 2.5 Å in comparison with previously reported KD-inhibitor structures, revealed an overlapping binding site in the ATP-binding pocket and common αC helix-out conformations. We identified distinct features of BAY-3827-bound structure which involve a disulfide bridge between αD helix Cys106 and activation loop residue Cys174. This may help to stabilize AMPK conformation upon BAY-3827 binding, where the position of activation loop Asn162 leads the DFG motif Phe158 to adopt a conformation facing the C-terminal kinase lobe displacing His137, leading to a broken regulatory spine and an inactive kinase state. BAY-3827 at 2.5-5 μM, but not structurally resembling inactive BAY-974, fully blocked AMPK activator (MK-8722)-mediated phosphorylation of ACC1 and inhibition of lipogenesis in hepatocytes. Unbiased transcriptome analysis in MK-8722-treated wild-type and AMPK-null hepatocytes revealed that >30% of MK-8722-stimulated AMPK-dependent genes could be downregulated by 5 μM BAY-3827. Based on its greater selectivity and potency substantiated by comprehensive molecular/cellular investigations. BAY-3827 is a powerful tool to delineate AMPK functions.

2025-07-28 | GSE290022 | GEO

Antarctic Marine Bacterioplankton Metagenome

Project description:Metagenome collected from Antarctic marine bacterioplankton

| PRJNA30543 | ENA