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RNA sequencing analysis of unchallenged, PBS injected and S. pneumoniae infected pcsk9 KO and WT zebrafish

ABSTRACT: RNA sequencing analysis of unchallenged, PBS injected and S. pneumoniae infected pcsk9 KO and WT zebrafish

PROVIDER: PRJNA694770 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13528200_1.fastq.gz	Fastqsanger.gz
	SRR13528200_2.fastq.gz	Fastqsanger.gz
	SRR13528201_1.fastq.gz	Fastqsanger.gz
	SRR13528201_2.fastq.gz	Fastqsanger.gz
	SRR13528202_1.fastq.gz	Fastqsanger.gz

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RNA sequencing analysis of unchallenged, PBS injected and S. pneumoniae infected pcsk9 KO and WT zebrafish

Project description:Purpose: S. pneumoniae infection in both zebrafish larvae and adult fish can be used to model pneumococcal bacteremia. Here, we used unchallenged, PBS injected and S. pneumoniae (T4) infected adult zebrafish to study the genome-wide role of pcsk9 in vivo in steady-state and upon immune system stimulation. Methods: Adult pcsk9 KO zebrafish and their WT siblings were infected with S. pneumoniae (3,370,000 CFU; SD 840,000 CFU) and their total liver RNA isolated at 1-day post infection. RNA-sequencing data was produced by NovaSeq. Data processing pipeline was built on Snakemake wrappers, and used STAR to quantify features from quality and adapter trimmed reads in gene level. Prior to the normalisation and differential gene expression analysis with DESeq2, the matrix of raw gene counts was prefiltered to keep only rows that have at least 10 reads total and then split by treatment to analyze each case separately. Result tables were annotated with biomaRt. Results: Snakemake preprocessing pipeline measured 32,520 genes against GRCz11, ENSEMBL release 97. 20,709 of them was used for statistical testing. Full result tables for each treatment were ranked by p-value and the normalized DESeq2 abundances in samples were included. The genes with BH-adjusted p-value <0.05 was considered differentially expressed. Conclusions: Our study identified up- and down-regulated genes in unchallenged, PBS injected and pneumococcal infected pcsk9 KO zebrafish liver compared to WT zebrafish.

2021-07-02 | GSE165508 | GEO

RT-qPCR analysis in zebrafish Viperin KO fish under VHSV infections

Project description:For this experiment, WT and Viperin KO fish were used and fish were injected with either PBS or VHSV and the gene expression was analyzed

2023-12-12 | GSE250036 | GEO

Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection.

Project description:To gain deeper insights into the relationship between Tau spreading and microglial response, we conducted a comprehensive analysis of microglial heterogeneity in K18-seeded P301L mice at 1 week, 1 month, and 3 months post-injection. We compared these findings with those from control groups: P301L mice injected with PBS and their non-transgenic counterparts, the FVB mice also subjected to PBS injection. For this purpose, we employed CITE-seq to investigate CD11b positive cells isolated from cerebellum and olfactory bulb-removed brains.

2024-05-29 | GSE253581 | GEO

Gene-expression profiling of SEPN1 knockout or wild type mice injected with either ERO1 or PBS

Project description:Endoplasmic reticulum (ER) and oxidative stress are two related phenomena that have important metabolic consequences. As many skeletal muscle diseases are triggered by oxidative stress, we explored the chain of events linking a hyper oxidized ER (which causes ER and oxidative stress) with skeletal muscle dysfunction. Using exon expression arrays we show that the combined genetic modulation of the two master ER redox proteins, selenoprotein N (SEPN1) and endoplasmic oxidoreductin 1 (ERO1), leads to an SEPN1-related myopathic phenotype due to excessive signalling of transforming growth factor (TGF)-beta. One-month-old WT and SEPN1 KO mice were intramuscularly injected with AAV2/1-ERO1a (an adeno-associated virus driving ERO1a) in three sites of the right gastrocnemius muscle and vehicle alone was injected into the contralateral muscle. The animals were sacrificed four-six weeks after injection and total RNA was isolated from muscle tissues using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Genechip Mouse Gene 2.1 ST arrays (Affymetrix) were used for whole genome gene-expression analysis of duplicated samples derived from WT and SEPN1 KO mice in presence of either ERO1 or PBS.

2016-10-01 | E-MTAB-4933 | biostudies-arrayexpress

PCSK9 deficiency results in a specific shedding of excess LDLR in female mice only: Role of hepatic cholesterol

Project description:PCSK9 promotes the lysosomal degradation of cell surface LDL receptor (LDLR). We analyzed how excess LDLR generated by PCSK9 deficiency is differently handled in male and female mice to possibly unveil the mechanism leading to the lower efficacy of PCSK9 mAb on LDL-cholesterol levels in women. Analysis of intact or ovariectomized PCSK9 knockout (KO) mice supplemented with placebo or 17β-estradiol (E2) demonstrated that female, but not male mice massively shed the soluble ectodomain of the LDLR in the plasma. Liver-specific PCSK9 KO or alirocumab-treated WT mice exhibit the same pattern. This shedding is distinct from the basal one and is inhibited by ZLDI-8, a metalloprotease inhibitor pointing at ADAM10/ADAM17. In PCSK9 KO female mice, ZLDI- 8 raises by 80 % the LDLR liver content in a few hours. This specific shedding is likely cholesterol-dependent: it is prevented in PCSK9 KO male mice that exhibit low intra-hepatic cholesterol levels without activating SREBP-2, and enhanced by mevalonate or high cholesterol feeding, or by E2 known to stimulate cholesterol synthesis via the estrogen receptor-α. Liver transcriptomics demonstrates that critically low liver cholesterol in ovariectomized female or knockout male mice also hampers the cholesterol-dependent G2/M transition of the cell cycle. Finally, higher levels of shed LDLR were measured in the plasma of women treated with PCSK9 mAb. PCSK9 knockout female mice hormonally sustain cholesterol synthesis and shed excess LDLR, seemingly like women. In contrast, male mice rely on high surface LDLR to replenish their stocks, despite 80 % lower circulating LDL.

2022-09-22 | GSE205008 | GEO

Atlas of miRNome variations in different dyslipidemic conditions: a study in C57Bl/6, Ldlr-KO, and Pcsk9-KO mice.

Project description:In this study, mice with different genotypes and fed diets with different lipid content were enrolled, aiming to set up an atlas of miRNA expression levels in different organs with a relevant role in lipid/lipoprotein metabolism. Specifically, three genotypes were investigated: C57Bl/6 mice as controls, together with mice knock-out (KO) for LDLr (low-density lipoprotein receptor) and for PCSK9 (proprotein convertase subtilisin/kexin type 9). LDLr and PCSK9 are both involved in LDL turnover, the former mediating LDL clearance [PMID: 19299327], the latter causing the degradation of the LDLr protein [PMID: 17080197]. As a result, LDLrKO mice, because of their impaired LDL catabolism, are hypercholesterolemic and prone to atherosclerosis development, particularly when fed high-fat, cholesterol-containing diets [PMID: 8349823; PMID: 8182121]. On the contrary, PCSK9KO mice, characterized by an accelerated LDL catabolism, are hypocholesterolemic and atherosclerosis resistant [PMID: 15805190]. miRNA expression was investigated in liver, intestine, aorta, white adipose tissue and brain of mice on both standard and Western diet.

2023-09-06 | GSE227578 | GEO

Transcriptome analysis of the injected Ppara-KO mice overexpressing TFEB specifically in liver

Project description:Expression data from Ppara (peroxisome proliferator activated receptor alpha) KO mice injected with TFEB specifically in liver. In order to identify the effects of TFEB overexpression together with Ppara absence on the liver transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the injected mice For the analysis on the injected Ppara-KO mice overexpressing TFEB, total RNA was extracted from the liver of three mice; RNA extracted from the liver of not-injected mice was used as control.

2013-04-20 | E-GEOD-41140 | biostudies-arrayexpress

Expression data of mRNA from hearts of mice injected with ETX or PBS

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Transcriptome analysis of the injected Ppara-KO mice overexpressing TFEB specifically in liver

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