Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide gene expression profiling of macrophages treated with novel 1,2,4-oxadiazole scaffold-based compounds

ABSTRACT: Genome-wide gene expression profiling of macrophages treated with novel 1,2,4-oxadiazole scaffold-based compounds

PROVIDER: PRJNA922037 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23021100.fastq.gz	Fastqsanger.gz
	SRR23021101.fastq.gz	Fastqsanger.gz
	SRR23021102.fastq.gz	Fastqsanger.gz
	SRR23021103.fastq.gz	Fastqsanger.gz
	SRR23021104.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 96

Similar Datasets

Genome-wide gene expression profiling of macrophages treated with novel 1,2,4-oxadiazole scaffold-based compounds

Project description:Background: Anti-tuberculosis drugs, mainly developed more than 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy (HDT) has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, we evaluated the impact of two host-directed compounds, namely MC3465 and MC3209, on the response of human monocytes-derived macrophages infected with Mycobacterium tuberculosis (MTB). Results: The expression of 181 genes was differentially regulated following MC3465 treatment (p-value < 0.05, log FC ≥ 0.5 and ≤ -0.5) after 4 h, with 53 being upregulated and 128 being downregulated. The expression of more genes was affected after 24h of treatment. 224 genes were upregulated and 652 genes downregulated. (p value < 0.05, log FC ≥ 0.5 and ≤ -0.5). We classified those differentially expressed genes by performing gene-set enrichment analysis using ClueGO cluster analysis. The gene set downregulated by MC3465 at 4 h was significantly enriched for genes associated with chemotaxis and cellular zinc ion homeostasis and cell chemotaxis. At 24 h, most of the downregulated genes belongs to the innate immune response and the cytokine response, with many genes belonging to the type I IFN pathway. Conclusions: Our results indicate that MC3465 alters zinc homeostasis in human macrophages.

2024-03-04 | GSE222412 | GEO

Lakshman scaffold

Project description:Lakshman Kund scaffold Metagenomic assembly

| PRJNA902919 | ENA

Imipridone anticancer compounds ectopically activate the ClpP protease and represent a new scaffold for antibiotic development

Project description:Imipridone anticancer compounds ectopically activate the ClpP protease and represent a new scaffold for antibiotic development

| PRJNA577699 | ENA

Imipridone anticancer compounds ectopically activate the ClpP protease and represent a new scaffold for antibiotic development

Project description:Systematic genetic interaction profiles can reveal the mechanism-of-action of bioactive compounds. The imipridone ONC201, which is currently in cancer clinical trials, has been ascribed a variety of different targets. To investigate the genetic dependencies of imipridone action, we screened a genome-wide CRISPR knockout library in the presence of either ONC201 or its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP or the mitochondrial intermediate peptidase MIPEP conferred strong resistance to both compounds. Biochemical and surrogate genetic assays showed that impridones directly activate CLPP and that MIPEP is necessary for proteolytic maturation of CLPP into a catalytically competent form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial as well as non-mitochondrial proteins. Prompted by the conservation of ClpP from bacteria to humans, we found that the imipridones also activate ClpP from Escherichia coli, B. subtilis and Staphylococcus aureus in biochemical and genetic assays. ONC212 and acyldepsipeptide (ADEP)-4, a known activator of bacterial ClpP, caused similar proteome-wide degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, B. subtilis, Enterococcus faecium) and Gram-negative species (E. coli, Neisseria gonorrhoeae). Moreover, ONC212 enhanced the ability of rifampin to eradicate antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.

2020-02-23 | GSE138894 | GEO

Gene expression profiles of RAW264.7 macrophage cells treated with Paeony root-derived compounds

Project description:Paeony root has long been used for its anti-inflammatory effects. In this study, the effects of albiflorin, paeoniflorin, and paeonol, compounds from paeony root, on gene expression profiles were examined in macrophages. The RAW264.7 macrophages were treated with LPS in the presence or absence of albiflorin, paeoniflorin, or paeonol. Global mRNA expression levels were detected by using an oligonucleotide microarray platform covering the mouse whole genome. Our results demonstrate that paeonol has extensive inhibitory effects on the regulation of inflammation-associated gene expression by LPS in macrophages. In addition, the predominant effect of paeonol among the tested compounds suggests that paeonol may be a major ingredient for the anti-inflammatory effect of paeony root. Keywords: RAW264.7; macrophage; inflammation; LPS; Paeony root components; dose response

2008-10-01 | GSE9632 | GEO

Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

Project description:This study investigated early host reactions to implanted materials to predict successful tissue regeneration with implant. Three kinds of scaffold, i.e., non-coat, collagen-coated, and PMB-coated porous polystylene scaffolds were implanted subcutaneously in mice dorsal area. Those scaffolds were used as bio-incomopatible materials, appropriate materials for tissue regeneration (bio active), and inappropriate to regenration (bio-inert) scaffolds. Seven days after implantation, scaffolds were explanted and total RNA was isolated from infiltrated host cells into scaffold by laser microdissection. Gene expressions of cells in collagen- and PMB-coated scaffold were normalized using results of non coat scaffold. Genes with more than 2-fold difference between collagen and PMB were picked up and narrowed to related keywords; inflammation, angiogenesis, wound healing, and mcrophage polarization. Among those genes, interluekin (IL)-1beta which promote both inflammation and wound healing was up-regulated in collagen-coated scaffold. On the other hand, IL-10 which suppress both inflammation and wound healing was up-regulated in PMB-coated scaffold. Angiogenesis-promoting genes were up-regulated and angiogenesis suppressve genes were suppressed in collagen. Up-regulation of IL-1b and the angiogenesis-relating genes inside the porous scaffolds are the possibly important factors for controlling tissue regeneration. Three-condition experiment, host cells infiltrated in non coat (reference), collagen-coated, and PMB-coated scaffolds. Two-microarray condition experiments, collagen vs. non coat and PMB coat vs. non coat. Hybridization: 2 replicates. Scanning: 3 replicates. Biological experiments: once.

2014-01-23 | E-GEOD-52053 | biostudies-arrayexpress

RNA-seq of human monocyte derived macrophages exposed to different atherogenic compounds

Project description:RNA-seq of human monocyte derived macrophages exposed to different atherogenic compounds

| PRJEB65093 | ENA

Profiling of novel p53-inducing compounds

Project description:We describe six novel lead compounds activating the p53 tumor suppressor pathway. Transcriptional profiling indicated that they invoked highly similar responses involving p53 and cell cycle pathways and DNA damage response signaling. Keywords: Stress response Six compounds and one vehicle control, with four biological replicates each, for a total of 28 samples.

2010-10-01 | E-GEOD-12666 | biostudies-arrayexpress

Nuclear scaffold and matrix attachment of HeLa chromatin

Project description:The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nuclear matrix respectively. We have mapped, by array CGH, the locations of attachment to each of these residual protein bodies relative to non-attached DNA along the entire length of human chromosomes 14, 15, 16, 17 and 18 in HeLa cells. LIS or 2 M NaCl solutions followed by restriction digestion with EcoR1 facilitates the separation from scaffold/matrix bound DNA from non bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of HeLa DNA. The expression profile of the HeLa cells used for aCGH analysis was also determined.

2010-05-22 | E-GEOD-13774 | biostudies-arrayexpress

Profiling of novel p53-inducing compounds

2010-10-01 | GSE12666 | GEO