Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CsDML OX Transcriptomes

ABSTRACT: Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between CsDML OX transgenic lines Wild Type Methods: Expression profiles were examined by RNA sequencing (RNA-Seq) in SD-induced (for 28 days) shoot apices of CsDML over-expressor and wild-type hybrid poplars. For RNA extraction, 25 apices from 25 trees of each WT, CsDML OX1 and CsDML OX3 genotypes were dissected under a binocular loupe to remove leaflets surrounding the shoot apical meristem Results: Using an optimized data analysis workflow, 318 differentially expressed genes (DEG) were identified in CsDML OX, among which 79 were found upregulated and 239 downregulated

ORGANISM(S): Populus tremula x Populus alba

PROVIDER: GSE87155 | GEO | 2017/09/23

SECONDARY ACCESSION(S): PRJNA343730

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The genes upregulated in WRKY45-ox rice relative to Nipponbare

Project description:WRKY45-overexpressing (WRKY45-ox) rice plants are extremely resistant to rice blast and bacterial leaf-blight diseases. To search for the genes that are potentially responsible for the strong resistance, we performed genome-wide gene expression analysis in WRKY45-ox rice. A microarray analysis using Agilent rice oligo microarray for approximately 42,000 rice genes identified 1,664 genes that are upregulated in WRKY45-ox rice compared with non-transformant rice cv. Nipponbare (NB). Analysis of the genes with altered expression in WRKY45-ox rice by a Gene ontology program (Agri GO; http://bioinfo.cau.edu.cn/agriGO/) revealed that several genes in the biosynthetic pathway for diterpenoid phytoalexins, for which anti-blast fungus activities have been reported, were upregulated in WRKY45-ox rice.

2013-12-31 | GSE48202 | GEO

Arabidopsis thaliana

Project description:Arabidopsis shoot apices dissection

| PRJNA85281 | ENA

RNA-Sequencing Analysis of ox-LDL-treated Peritoneal Macrophages Transcriptomes

Project description:Since previous stduies demostrated that oxidized phospholipids function as caspase-11 agonists to induce noncanonical inflammasome activation in immune cells and the levels of oxidized phospholipids derived from ox-LDL are largely elevated in atherosclerotic lesions. Purpose:RNA-Sequencing analysis of ox-LDL-treated peritoneal macrophages transcriptomes.Methods and results:The principal component analysis gene expression profiles of the control and ox-LDL-treated groups were clearly distinct. Among the DEGs that met the cutoff criteria of a -log10(false discovery rate (FDR)) > 2 and |log2(fold change (FC)| > 2. A total of 1,388 downregulated and 855 upregulated genes were identified. GSEA showed that the dominant upregulated pathways in ox-LDL-treated macrophages were associated with the IL-1-mediated signaling pathway, response to cytokine stimulus, and granulocyte migrationwe discovered that caspase-11-mediated inflammation signaling was significantly activated in ox-LDL-treated peritoneal macrophages.Conclusions：we verified caspase11associated inflammatory signaling was significantly activated in ox-LDL-treated macrophages.

2021-05-19 | GSE171413 | GEO

Transcription profiling of Arabidopsis wild type and myo mutant shoot apices

Project description:Transcription profiling of shoot apices of the myo mutant was compared with shoot apices of WT (background Ler).

2009-07-22 | E-MEXP-1735 | biostudies-arrayexpress

Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX

Project description:Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX

| PRJNA638540 | ENA

The genes upregulated in WRKY45-ox rice relative to Nipponbare

2013-12-31 | E-GEOD-48202 | biostudies-arrayexpress

Protective Effects of Mitochondrial Fission Inhibition on Ox-LDL Induced VSMC Foaming via Metabolic Reprogramming

Project description:Atherosclerosis (AS) is one of the most common diseases in middle-age and elderly population. Lipid metabolism disorder induced foaming of vascular smooth muscle cell (VSMC) is an important pathological process of AS. Mitochondria plays an important role in lipids metabolism. While it is not known whether regulating mitochondrial function can protect ox-LDL induced VSMC foaming via metabolic reprogramming. With ox-LDL induced mouse model of VSMC injury, the injury effect of ox-LDL and the protective effect of mdivi-1, the mitochondrial fission inhibitor on mitochondrial morphology and function of VSMC, and the formation of lipid droplet were observed. With metabonomics and proteomics techniques, the main lipid metabolites and regulation proteins were identified. The results showed that Ox-LDL induced a significant mitochondrial fission and fragmentation of VSMC, and mitochondrial function disorder along with lipid deposition and foaming. Mdivi-1 significantly antagonized the damage effect of ox-LDL on mitochondrial morphology and function of VSMC, and blocked the lipid deposition. Metabonomics analysis found 848 different metabolites between ox-LDL and mdivi-1 treatment group, in which the lipid metabolites were the main, and heptadecanoic acid, palmitoleic acid and myristic acid were the critical metabolites changed most. Proteomics results showed that there were 125 differential expressed proteins between ox-LDL and mdivi-1 treatment, acetyl -CoA carboxylase1 and fatty acid synthase were the main differential expressed proteins. This study suggest that Mitochondrial fission plays an important role in VSMC lipid deposition and foaming. Inhibition of mitochondrial fission may effectively fight against ox-LDL induced lipid deposition and foaming of VSMC via improving mitochondrial function and metabolic reprogramming. This finding provides a new insight for prevention and treatment of AS.

2022-10-14 | PXD035671 | Pride

Expression data from bladder cancer cells T24 treated with ox-LDL or vehicle

Project description:Target genes regulated by ox-LDL treatment in bladder cancer cells T24 were identified by microarrays. In this dataset, we include the expression data obtained from bladder cancer cells T24 starved with serum-free medium and then treated with 20 μg/mL ox-LDL or vehicle for 24 h. These data are used to obtain genes that are differentially expressed in response to ox-LDL treatment.

2022-02-18 | GSE134530 | GEO

Transcription profiling of Arabidopsis TOC1-ox transcriptional networks

Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 overexpressor plants (TOC1-ox). Experiment Overall Design: Comparisons of WT and TOC1-ox. Three biological replicates synchronized under 12-hour light:12-hour dark (LD) cycles for 12 days. Samples were collected at Zeitgeber Time 15 (ZT15).

2009-09-18 | E-GEOD-18007 | biostudies-arrayexpress

Genome-wide analysis of TOC1-ox transcriptional networks

2009-09-09 | GSE18007 | GEO