We showed that KLF-1 is needed for longevity of isp-1(qm150);ctb-1(qm189) mutant specifically in adulthood. We aimed to determine the expression changes that occur specifically upon adulthood klf-1 RNAi compared to developmental RNAi that did not affect the lifespan of isp-1(qm150);ctb-1(qm189) mutant.
No associated publication
No sample metadata fields
View SamplesMicroarray analysis of the changes in transcript abundance in cell culture and shoot
Heterogeneity of the mitochondrial proteome for photosynthetic and non-photosynthetic Arabidopsis metabolism.
None
Specimen part
View SamplesTranscript abundance profiles were examined over the first 24 hours of germination in rice grown under aerobic conditions.
Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity.
None
Specimen part, Time
View SamplesEffect of high light on directly exposed and shaded, distal Arabidopsis leaf tissue
Systemic and intracellular responses to photooxidative stress in Arabidopsis.
None
No sample metadata fields
View SamplesIn Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B. In vitro and in vivo experiments indicated that snR39 is normally processed from the lariat of RPL7A, suggesting that the expressions of RPL7A and snR39 are linked. In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously. The results presented here reveal a new role of yeast RNase III in the processing of intron-encoded snoRNAs that permits independent regulation of the host mRNA and its associated snoRNA.
Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals.
No sample metadata fields
View SamplesGenome-wide association studies (GWAS) have identified genes in lipid metabolism,inflammation and vesicular trafficking pathways as risk factors for late onset Alzheimer disease (LOAD). The mechanism by which they cause AD and their relationship to the amyloid cascade affected by genes causing early onset familial AD is unknown. Unproven hypotheses are that these LOAD genes modulate the amyloid cascade itself or downstream targets affected by this cascade.If so, it is likely that these genes and/or other genes in the same pathways may show alterations in their expression as an early consequence of misprocessing of amyloid precursor protein (APP) and accumulation of amyloid -peptides (A). We report that in three independent APP transgenic mouse models of AD, multiple genes in lipid and inflammation pathways show very early changes in mRNA and protein expression. Many of these changes are reversed by treatment with LXR agonists, which regulate transcription of genes in lipid/inflammation pathways, and which we have previously shown can reverse the cognitive deficits and neuropathology in Tg2756 mice. These results suggest that changes in lipid and inflammation pathways are likely to be very early consequences of APP misprocessing and A accumulation in AD. Moreover, genetic variants within these pathways might affect risk for AD by modulating this early response. These pathways are likely to contain biomarkers of early disease and targets for therapies.
No associated publication
Age, Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Genomic impact of transient low-dose decitabine treatment on primary AML cells.
Sex, Age, Specimen part, Disease, Treatment
View SamplesAcute myeloid leukemia (AML), and other myeloid malignancies, are frequently treated with hypomethylating agents like decitabine. Alterations in the epigenome, induced by decitabine, are likely to result in gene expression changes. The effects of decitabine have not been systemically studied using primary AML samples.
Genomic impact of transient low-dose decitabine treatment on primary AML cells.
Specimen part, Disease, Treatment
View SamplesSex chromosomes are characterized by a non-random content of genes with preferential expression in one sex. The mechanisms which are responsible for this phenomenon are, however, largely unresolved. To elucidate selective forces shaping the Z chromosome gene content in chicken, we analyzed microarray data from adult and embryonic gonads (the latter already available in GEO Series GSE8693).
No associated publication
No sample metadata fields
View SamplesThis study compared the photosynthetic performance and the global gene expression of the winter hardy wheat Triticum aestivum cv Norstar grown under non-acclimated (NA) or cold-acclimated (CA) condition at either ambient CO2 or elevated CO2 (EC). CA Norstar maintained comparable light saturated and CO2 saturated rates of photosynthesis but lower quantum requirements for photosystem II and non photochemical quenching relative to NA plants even at EC. Neither NA nor CA plants were sensitive to feedback inhibition of photosynthesis at EC. Global gene expression using microarray combined with bioinformatics analysis revealed that genes affected by EC were 3 times higher in NA (1022 genes) compared to CA (372 genes) Norstar. The most striking effect was the down-regulation of genes involved in the plant defense responses in NA Norstar. In contrast, cold acclimation reversed this down regulation due to the cold induction of genes involved in plant pathogenesis resistance, and cellular and chloroplast protection. These results suggest that EC have less impact on plant performance and productivity in cold adapted winter hardy plants in the northern climates compared to warmer environments. Selection for cereal cultivars with constitutively higher expression of biotic stress defense genes may be necessary under EC during the warm growth period and in warmer climates.
Long-term growth under elevated CO2 suppresses biotic stress genes in non-acclimated, but not cold-acclimated winter wheat.
Specimen part
View Samples