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Global gene expression of Ad-OSCAR and subsequently 5-ASA treated mice with Control mice

ABSTRACT: Global gene expression of Ad-OSCAR and subsequently 5-ASA treated mice with Control mice

PROVIDER: PRJNA853381 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19879020_1.fastq.gz	Fastqsanger.gz
	SRR19879020_2.fastq.gz	Fastqsanger.gz
	SRR19879021_1.fastq.gz	Fastqsanger.gz
	SRR19879021_2.fastq.gz	Fastqsanger.gz
	SRR19879022_1.fastq.gz	Fastqsanger.gz

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Global gene expression of Ad-OSCAR and subsequently 5-ASA treated mice with Control mice

Project description:To examine the effects of Oscar and its inhibitor 5-ASA on articular cartilage, we established OSCAR overexpressed chondrocytes with adenovirus and treated 5-ASA subsequently. Gene expression profiling analysis was performed using articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq.

2023-06-30 | GSE207056 | GEO

Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice.

Project description:Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice.

| PRJNA615179 | ENA

Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice.

Project description:Purpose: RNA sequencing (RNA-Seq) analyses of articular cartilage obtained after DMM surgery in Oscar-/- and WT mice. The purpose of this experiment was to demonstrate how the deficiency of Oscar gene affects downstream signal transduction in articular cartilage. Methods: Articular cartilage mRNA profiles of 10-weeks-old wild-type (WT) and Oscar knockout (Oscar−/−) mice were performed for the destabilization of the medial meniscus (DMM) and each cartilage tissue sample was harvested from two time-points (2- and 4-weeks after surgery). Sequencing libraries were prepared according to the manufacturer’s instructions (TruSeq Stranded mRNA Library Prep Kit; Illumina, San Diego, CA, USA). Paired-end sequencing of 101-mer read length was performed using a HISEQ 2500 sequencing system (Illumina). The sequencing quality of raw FASTQ files was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and adapter sequences in reads were eliminated using BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools/). Results: Usinig RNA-Seq data in articular cartilage tissues from WT and Oscar–/– mice subjected to sham or DMM surgery and each cartilage sample obtained from 2- and 4-week time points after surgery, respectively. And we found that significantly enriched pathways in the 1270 common genes. Conclusions: Our study represents the Oscar gene deficiency analysis of articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-03-26 | GSE147529 | GEO

Ad vectors in C3KO mice

Project description:Replication-deficient adenovirus (Ad) type 5 capsids induce potent host innate immune responses. One system pivotal in host innate immune defense is the complement system. Intriguingly, excessive or inappropriate complement activation can result in extreme tissue damage and systemic inflammatory responses similar to those noted immediately after high dose systemic Ad vector injections. To determine if the complement system has a significant role in intensifying Ad-associated acute toxicities, we compared complement deficient (C3-knockout (KO)) mice responses to those of wild type (WT) mice following systemic challenge with Ad vectors. We noted not only thrombocytopenia and rapid increases in plasma IL-6, IFN-γ, TNF-α, and IL-12 levels previously reported after high dose Ad injections into WT mice, but also induction of cytokines IL-2, IL-4, IL-5 and IL-10, G-CSF and GM-CSF, and chemokines KC (CXCL1) and MIP-1. This expanded innate response “profile” was significantly blunted in Ad injected C3-KO mice, with a near complete avoidance of thrombocytopenia. Further validation for complement’s critical role in perturbing these innate responses against Ad were noted after comparison of gene specific RNA transcription levels in C3-KO to WT mice livers. Finally, these disparities were not attributed to a diminished ability of the Ad vectors to transduce C3-KO mice hepatocytes. These results suggest that Ad capsid interaction with the mammalian complement system may exacerbate the toxicity of systemic Ad injections, and thus represents a future target for manipulation in efforts to improve the efficacy and safety profile of Ad mediated gene delivery. Keywords: adenovirus, complement system, time course, innate immune response, toxicity

2006-02-15 | GSE4128 | GEO

Inhibiting neutrophils activation by long-term administration of 5-amino salicylic acid reduces colitis-associated colorectal tumor burden in ApcMin/+ mice

Project description:Objective The risk of ulcerative colitis (UC)-associated colorectal cancer (CRC) increases with the duration of UC. Oral 5-aminosalicylic acid (5-ASA) formulations are the first-line treatment for mild-to-moderate UC; nevertheless, preventive effect of oral 5-aminosalicylic acid (5-ASA) formulations on UC-associated CRC remains unsolved. We investigated the impact of 5-ASA to colitis-associated neoplasia in C57BL/6J-ApcMin heterozygous (ApcMin/+) mice. Design ApcMin/+ mice exposed to 1.5 w/v% dextran sulfate sodium (DSS) ad libitum for 3 days followed by 25 days of tap water to develop colitis-associated neoplasia. Mice were intracolorectally administrated with 5-ASA to evaluate the effects on the number of tumors. The mechanism of action was presumed by microarray analysis using in vivo samples and was confirmed by in vitro culture of HT-29, a human colorectal adenocarcinoma cell line with supernatant of human primary neutrophils. Results A remission between acute and recurrent episodes of diarrhea, which were ameliorated by 5-ASA treatment were observed in this model. The number of tumors was reduced by continuous 5-ASA administration in this model. This reduction was abolished by withdrawal of 5-ASA in remission period compared to continuous 5-ASA administration. Microarray analysis revealed that neutrophils were involved in the protective mechanism of 5-ASA against proliferation of tumors. Additionally, calprotectin production from human primary neutrophil as activation marker was strongly correlated with proliferation of HT-29.

2019-06-26 | GSE83749 | GEO

Expression data from Paneth cells isolated from mice on calorie restricted or ad libitum diet

Project description:Paneth cells recide in the intestinal crypt bottom and are part of the innate immunity and of the intestinal stem cell niche. We used microarrays to detail the global changes in gene expression following reduced calorie intake. Mice were kept on ad libitum or calorie restricted (60% of calories of ad libitum) diets for 4-7 weeks and paneth cells were isolated using flowcytometry

2012-04-11 | E-GEOD-37209 | biostudies-arrayexpress

Transformation of mature adipocytes to liposarcoma in Ad/NICD mice

Project description:Analysis of inguinal white adipose tissue (WAT) and liposarcoma (LPS) isolated from Notch1 overexpression mice (Ad/NICD). Results provide insight into molecular mechanisms underlying tumorigenic transformation of Ad/NICD mature adipocytes

2016-08-28 | GSE80433 | GEO

Brain-derived and circulating EVs from hypoperfused mice, early AD and mixed dementias

Project description:In this project we provide profiling of brain-derived and circulating EVs LC-MS/MS data from mice subjected to bilateral common carotid stenosis (BCAS) and Sham controls. Furthermore, data from brain-derived EVs of early AD and mixed dementias (AD+CVD) is also provided.

2021-09-08 | PXD009093 | Pride

Next-generation sequencing analysis of microglia from AD and Calhm2 cKO/AD mice

Project description:Next-generation sequencing analysis of microglia from AD and Calhm2 cKO/AD mice

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Expression data from PDK4 overexpressing (Ad-PDK4 infected) and control (Ad-control infected) mouse liver

Project description:We identified PDK4 as a gene with adaptive transcriptional response to chemical stress. Although PDK4 is an energy resource regulator induced by starvation, expression of other fasting-inducible genes was unaffected, indicating additional physiological role of PDK4 for liver adaptation to the chemical stress. We used microarrays to determine genes with altered transcriptional level by PDK4 overexpression. Mice were infected with Ad-control (empty adenovirus vector) or Ad-PDK4 (PDK4 overexpressing adenovirus vector) at a dose of 10^9 PFU/mouse by tail vein injection. 3 days after the infection, mice were sacrificed for RNA preparation from the liver. Ad-control infected = 4, Ad-PDK4 infected = 3. Specimens from mice of each group were pooled, and 10 ug RNA from each pool was used for cRNA synthesis.

2010-12-25 | E-GEOD-22534 | biostudies-arrayexpress

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