Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12352 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR319677_1.fastq.gz | Fastqsanger.gz | |||
| DRR319677_2.fastq.gz | Fastqsanger.gz | |||
| DRR319678_1.fastq.gz | Fastqsanger.gz | |||
| DRR319678_2.fastq.gz | Fastqsanger.gz | |||
| DRR319679_1.fastq.gz | Fastqsanger.gz |
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Project description:The bioactive sphingolipid ceramide, generated by ceramide synthase, is an adaptive stress effector induced in response to various stress stimuli such as aging. In fact, ceramide synthase (CerS) was first discovered in yeast as a longevity assurance gene (LAG1), as the reduced ceramide generation consequent to LAG1 deletion increased longevity. There are six homologues of mammalian LAG1/ceramide synthases (CerS1-6) that generate ceramides with different fatty acid chain lengths with distinct functions and hydrophobicity. Ceramide can be metabolized by sphingosine kinase 1 or 2 for the generation of pro-survival sphingosine 1-phosphate (S1P), which enhances immune cell egress to the blood stream, activating immune function. Ceramide is known to induce mitophagy and cell death. Here we investigated the role of this sphingolipid pathway in immune function, specifically T cell functions, via high throughput expression profiling.
2021-01-01 | GSE148498 | GEO
Project description:We have used human umbilical vein endothelial cell line (HUVEC) as a model to investigate the effect of ultrasound (US) activated micro-bubbles on sensitizing the tumour response to radiation and to check the implication of this approach on gene expression. The use of micro-bubbles in cancer therapy is a novel approach that is being recently investigated, and patterns of gene expressions were not yet characterized. Gene analysis has identified about 19,264 genes; where, 239 – 517 genes have shown more than two folds up-regulation in response to the different treatments. This included a number of genes that are known to be involved in apoptosis and ceramide-induced apoptosis pathways, such as Sphingomyelin phosphodiesterase 2, neutral sphingomyelinase (SMPD2), sphingomyelin phosphodiesterase 1, acid lysosomal (ASM; SMPD1), UDP-galactose ceramide galactosyltransferase (UGT8), cytochrome c oxidase (COX6B1), Caspase-9 and mitogen-activated protein kinase kinase 1 (MAP2K1). To verify these results, we have performed Real time RT-PCR, which indicated an up-regulation that ranged from 2 to 200 folds, specifically in the combined treatment of US, 3.3% micro-bubbles and 8 Gy. The observed higher levels of expression of UGT8, SMPD2 and Caspase 9-alpha when compared to the control or to radiation only indicated the involvement of ceramide, which possibly induces apoptosis . These results support the hypothesis that micro-bubbles play a role in increasing sensitization to radiation, and can prove to be an effective cancer therapeutic approach. Gene analysis has identified about 19,264 genes; where, 239 – 517 genes have shown more than two folds up-regulation in response to the different treatments. This included a number of genes that are known to be involved in apoptosis and ceramide-induced apoptosis pathways, such as Sphingomyelin phosphodiesterase 2, neutral sphingomyelinase (SMPD2), sphingomyelin phosphodiesterase 1, acid lysosomal (ASM; SMPD1), UDP-galactose ceramide galactosyltransferase (UGT8), cytochrome c oxidase (COX6B1), Caspase-9 and mitogen-activated protein kinase kinase 1 (MAP2K1). To verify these results, we have performed Real time RT-PCR, which indicated an up-regulation that ranged from 2 to 200 folds, specifically in the combined treatment of US, 3.3% micro-bubbles and 8 Gy. The observed higher levels of expression of UGT8, SMPD2 and Caspase 9-alpha when compared to the control or to radiation only indicated the involvement of ceramide, which possibly induces apoptosis . These results support the hypothesis that micro-bubbles play a role in increasing sensitization to radiation, and can prove to be an effective cancer therapeutic approach.
2009-08-27 | E-GEOD-17525 | biostudies-arrayexpress
Project description:Reactive oxygen species (ROS) generated as by-products of metabolism can induce stochastic damage to cellular components including DNA. A localised oxidative damage may arise during transcriptional activation at promoters of protein coding genes. ROS are generated during oxidative demethylation of histones and 5-methyl cytosine in promoter CpG clusters. ROS induced oxidation of DNA bases, mainly 7,8-dihydro-8-oxoguanine (8-oxoG) is normally resolved through a well characterised repair pathway where the oxidised base is first removed by components of base excision repair (BER) pathway, and the resulting breaks in the DNA backbone are subsequently repaired by the single-strand repair (SSBR) machinery that includes TDP1 and XRCC1. In this project we have identified the role of a putative mitotic assembly protein, TDIF in ROS induced single strand break repair. Using semi-quantitative LC-MS/MS and biochemical assays we show that the long isoform of TDIF specifically interacts with SSBR machinery after oxidative damage.
2022-10-12 | PXD018002 | Pride
Project description:We determined the profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide, and their quantitative differences between control and glaucomatous trabecular meshwork (TM) derived from human donors.
2017-05-26 | ST000613 | MetabolomicsWorkbench
Project description:The cleavage of sphingoid base phosphates by sphingosine-1-phosphate (S1P) lyase to produce phosphoethanolamine and a fatty aldehyde is the final degradative step in the sphingolipid metabolic pathway. We have studied mice with an inactive S1P lyase gene and have found that, in addition to the expected increase of sphingoid base phosphates, other sphingolipids (including sphingosine, ceramide, and sphingomyelin) were substantially elevated in the serum and /or liver of these mice. This latter increase is consistent with a reutilization of the sphingosine backbone for sphingolipid synthesis due to its inability to exit the sphingolipid metabolic pathway. Furthermore, the S1P lyase deficiency resulted in changes in the levels of serum and liver lipids not directly within the sphingolipid pathway, including phospholipids, triacyglycerol, diacylglycerol, and cholesterol. Even though lipids in serum and lipid storage were elevated in liver, adiposity was reduced in the S1P lyase-deficient mice. Microarray analysis of lipid metabolism genes in liver showed that the S1P lyase deficiency caused widespread changes in their expression pattern. These results demonstrate that S1P lyase is a key regulator of the levels of multiple sphingolipid substrates and reveal functional links between the sphingolipid metabolic pathway and other lipid metabolic pathways that may be mediated by shared lipid substrates and changes in gene expression programs. The disturbance of lipid homeostasis by altered sphingolipid levels may be relevant to metabolic diseases. Experiment Overall Design: RNA samples from liver for three sphingosine-1-phosphate lyase knock-out and three WT mice.
2010-02-05 | E-GEOD-18745 | biostudies-arrayexpress
Project description:The genome-wide target genes of transcription factors MYC2 and MYC3 were determined in etiolated (dark-grown) seedlings of Arabidopsis thaliana. Chromatin immunoprecipition of MYC2 and MYC3 was performed as described in O’Malley et al (2016; doi: 10.1016/j.cell.2016.04.038), using transgenic A. thaliana expressing MYC2::YpET and MYC3::YpET fusion proteins from their native promoters, generated by recombineering (Gimenez-Ibanez et al. 2017; doi: 10.1111/nph.14354 ). Three-day old etiolated seedlings were treated with methyl JA for 2 h (as described in Schweizer et al., 2013), then harvested for ChIP-Seq.
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Project description:Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of lectin receptor kinase 1 after elicitation with oral secretions of Manduca sexta larvae.
2011-11-23 | GSE29905 | GEO
Project description:To determine the differential profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide and their quantitative differences between trabecular meshwork (TM) and aqueous humor (AH) derived from normotensive and hypertensive intraocular pressure states of DBA/2J mice.
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Project description:Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavages by small RNAs. Here we developed an extension module based on a deep learning convolutional neural network (CNN) in a machine learning environment to discriminate false from true cleavage sites applied on datasets from potato (Solanum tuberosum, St) and the oomycete pathogen Phytophthora infestans (Pi). The core of the CNN module is a stochastic gradient descent optimizer with cyclical learning rate (CLR) which together with Bayesian optimization scored a validation accuracy of 100%. To verify the recognition of cleavage sites we applied the module on Arabidopsis thaliana microRNA cleavages. Our module managed to recognize all cleavages, confirming the reliability of the module. When applying this new model to evaluate our data, 7.3% of all cleavage windows represented true cleavages distributed as 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the potato-P. infestans interaction is complex with uneven sRNA production and cleavage regions. In total, 222 endogenous Pi-sRNAs, 565 endogenous St-sRNAs, 91 trans-acting Pi-sRNAs and 14 trans-acting St-sRNAs were discovered from our datasets. Groups of self-regulatory sRNAs, and sRNAs generated from effector sequences like RXLR and Crinklers suggest dual effector functions. In the potato genome, resistance genes were most targeted mainly as self-regulation but also as results of a trans-action event. Our new analytic model is freely accessible for anyone working on complex biological systems.
2021-05-05 | GSE163382 | GEO
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2017-10-05 | GSE93644 | GEO