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5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RIP-seq whole]

ABSTRACT: To evoke further attention to the potential hazard of increasingly accumulative blue light exposure, we construct a series of in vivo Drosophila models employed for multi-omics analyses. This project includes the identification results of untargeted metabolome quantification by LC-MS/MS and the Input and m6A IP data of MeRIP-seq of w1118 male adult whole flies.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE197395 | GEO | 2023/11/08

REPOSITORIES: GEO

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5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RNA-seq head]

Project description:To evoke further attention to the potential hazard of increasingly accumulative blue light exposure, we construct a series of in vivo Drosophila models employed for multi-omics analyses. This project includes the RNA-seq data of w1118 male adult heads.

2023-11-08 | GSE197370 | GEO

5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila [RNA-seq whole]

2023-11-08 | GSE197382 | GEO

RNA-Seq of human fibroblasts exposed to X-ray radiation

Project description:This dataset is composed by the transcriptomic, proteomic and phosphoproteomic profile of primary human fibroblasts exposed to two different doses of radiation: an acute X-ray radiation dose, and an accumulative X-ray radiation dose. These data were employed to apply and evaluate different computational approaches to model and infer cellular signaling processes through the combination of prior knowledge and omic data. We employed RNA-Seq and Mass Spectrometry (MS) to generate the transcriptomic and proteomic data from the RNA and protein samples, respectively.

2023-01-01 | E-MTAB-10456 | biostudies-arrayexpress

Genome-wide analysis of gene expression in human iPSCs and NSCs engineered by safe-harbor TALEN-mediated gene targeting

Project description:Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs. Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.

2014-09-01 | E-GEOD-55975 | biostudies-arrayexpress

5' UTR-dependent m6A methylation regulates aging and circadian rhythms in Drosophila

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-08 | GSE197397 | GEO

<i>Period2</i> 3'-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation.

Project description: Not available

| S-EPMC5651750 | biostudies-literature

MeRIP, RIP and RNA Sequencing of the H1299 stable cell lines which the endogenous YTHDF2 was silenced by a short hairpin RNA targeting YTHDF2 3’UTR (shYTHDF2) and then re-expressed Flag-tagged YTHDF2-WT orYTHDF2-K571R

Project description:SUMOylation affects many aspects of target proteins such as activity, stability, localization and protein-protein interactions. We have found that SUMOylation of YTHDF2 increased its binding activity with m6A-RNAs by using different experimental approaches. To confiremd this conclusion,the analysis of RIP-seq, MeRIP-seq and RNA-seq in H1299-shYTHDF2 cells re-expressing YTHDF2-WT and YTHDF2-K571R was performed. MeRIP+RIP targets showed lower binding affinities in the mutant YTHDF2-K571R when compared with YTHDF2-WT. Compared to the control group, the binding capacities of YTHDF2 to RIP targets in treated group with either 2-D08 or GA were decreased, especially to MeRIP+RIP targets. Moreover, SUMOylated YTHDF2 promoted m6A-RNAs degradation. Combined analysis of RNA-seq, RIP-seq and MeRIP-seq showed that the mRNA levels were up-regulated in shYTHDF2 stable cells re-expressing YTHDF2-K571R compared with those in re-expressing YTHDF2-WT.

2021-01-26 | GSE164917 | GEO

Characterization of the redox proteome of Drosophila melanogaster S2 cells and w1118 fly eyes.

Project description:Reactive oxygen species (ROS) serve as intracellular signaling molecules; however, in excess ROS molecules are damaging to biomacromolecules such as DNA, lipids, and proteins. The excess accumulation of ROS leads to oxidative stress, disrupting redox homeostasis in the cell and has been linked with aging and neurodegenerative disease. The eye is particularly vulnerable to oxidative stress due to the tissue’s high energy demand and generation of ROS by products. In proteins, the thiol group on cysteine residues is susceptible to oxidation. Cysteine residues have multiple oxidation states that can be classified into two categories—reversible and irreversible. Irreversible oxidation states include sulfinic and sulfonic acids, which may alter or impair the activity of the protein depending on the position of the cysteine residue. In contrast, reversible oxidation states include sulfenic acid or inter- and intramolecular disulfides, and can often function as redox sensors in the cell. Here, we sought to evaluate how increasing amounts of oxidative stress alters the redox proteome landscape in Drosophila. To characterize the redox proteome, we developed an iodoTMT-multiplex isolation, labeling, and enrichment method to identify cysteine availability and potential oxidation in both S2 cells and w1118 fly eyes. To do this, we exposed S2 cells to 20mM H2O2 relative to control (untreated), and w1118 flies to prolonged blue light versus an untreated control, followed by redox proteome profiling with iodoTMT-sixplex reagents.

2023-04-27 | PXD034050 | Pride

Microarray experiment to identify gene expression changes in response to Phenobarbital treatment and CncC overexpression in Drosophila.

Project description:Transcriptional profiling of mature adult w1118 males treated with phenobarbital compared to controls and heat treated HS-CncC flies compared with heat treated w1118 flies.

2011-11-29 | GSE30087 | GEO

Expression profile for Drosophila Sox14 at onset of metamorphosis

Project description:We used microarray analysis of RNA obtained from w1118 and w1118;sox14L1/sox14L1 animals staged at pupariation to identify genes regulated by Drosophila Sox14 at the onset of metamorphosis.

2010-07-31 | GSE23355 | GEO

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