E-GEOD-10479
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA107921
PROVIDER: E-GEOD-10479 | ExpressionAtlas | 2014-07-03
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-10479-analysis-methods.tsv | Tabular | |||
| E-GEOD-10479-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-10479-configuration.xml | Xml | |||
| E-GEOD-10479-percentile-ranks.tsv | Tabular | |||
| E-GEOD-10479-zoomifications-log.tsv | Tabular |
Items per page: 5 1 - 5 of 65 |
Similar Datasets
Project description:Primary outcome(s): Analysis of expression induced genes. Quantitative analysis by qPCR.
| 2645606 | ecrin-mdr-crc
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Significant differential expression genes from HUVECs induced by bg-CAT
| PRJNA107921 | ENA
Project description:Interventions: Gold Standard:tissue or cytopathology;Index test:secreted LncRNA
Primary outcome(s): Differential expression of LncRNA in peripheral blood exosomes of patients
Study Design: Single arm
| 2739486 | ecrin-mdr-crc
Project description:Differential analysis of testosterone induced genes by peritubular cells
| PRJNA325530 | ENA
Project description:Here we present a mathematical model of IL-6-induced JAK1-STAT3 signaling that quantitatively links physiological IL-6 concentrations to the dynamics of IL-6-induced signal transduction and expression of target genes in hepatocytes. The mathematical model consists of coupled ordinary differential equations (ODE) and the model parameters were estimated by a maximum likelihood approach, whereas identifiability of the dynamic model parameters was ensured by the Profile Likelihood. Using model simulations coupled with experimental validation we could optimize the long-term impact of the JAK-inhibitor Ruxolitinib, a therapeutic compound that is quickly metabolized.
2023-07-05 | MODEL2307050001 | BioModels
Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
| 98681 | ecrin-mdr-crc
Project description:We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3â??-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, HMGB1, KLF12 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of HMGB1, KLF12 and CIT was detected in advanced stages of cancer. This study provides new insights and a comprehensive catalogue of p53-mediated regulations and p53 DNA binding in CRC cells.
2016-05-24 | MSV000079767 | MassIVE
Project description:Bat cells and tissue have elevated basal expression levels of antiviral genes commonly associated with IFNα signalling. Here we show IRF1,3 and 7 levels are elevated in most bat tissues and that basally, IRFs contribute to the expression of type I IFN ligands and high expression of Interferon Regulated Genes (IRGs). CRISPR KO of IRF 1/3/7 in cells reveal distinct subsets of genes affected by each IRF in an IFN-ligand signalling dependent and largely independent manner. As the master regulators of innate immunity, the IRFs, control the kinetics and maintenance of the IRG response and play essential roles in response to IAV, HSV1, PRV3M and MERS-CoV infection. With its differential expression compared to human, this highlights a critical role for basal IRF expression in viral responses and potentially immune cell development in bats with relevance for IRF function in human biology.
2020-10-23 | PXD021982 | JPOST Repository
Project description:Clubroot disease, caused by Plasmodiophora brassicae Woronin results in severe yield losses in Brassica crops, including canola. Silicon (Si) mitigates several stresses and enhances plant resistance to phytopathogens. We investigated the effects of Si on clubroot disease symptoms in canola at two concentrations of Si (Si1.0 and Si0.5). In addition, the effects of Si on P. brassicae-induced gene expression, endogenous levels of phytohormones and metabolites were also studied. Si application reduced clubroot symptoms and improved plant growth under greenhouse conditions. Pathogen-induced transcript-level changes were affected by Si treatment to P. brassicae with genes related to antioxidant activity, phytohormone biosynthesis and signalling, nitrogen metabolism and secondary metabolism exhibiting differential expression. Endogenous levels of several phytohormones (e.g., auxin, cytokinin, salicylic acid and abscisic acid), amino acids and secondary metabolites (e.g., glucosinolates) were affected by Si. This is the first report that Si ameliorates clubroot symptoms and its possible mode of action.
2022-12-12 | ST002406 | MetabolomicsWorkbench