Whole Genome Sequencing Cats
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34021 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3485780_1.fastq.gz | Fastqsanger.gz | |||
| ERR3485780_2.fastq.gz | Fastqsanger.gz | |||
| ERR3485781_1.fastq.gz | Fastqsanger.gz | |||
| ERR3485781_2.fastq.gz | Fastqsanger.gz | |||
| ERR3485782_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Next generation sequencing for the feline transcriptome (mRNA and microRNA profiles) was carried out using myocardial samples from female and male young healthy cats, adult healthy cats, and cats with hypertrophic cardiomyopathy.
2025-07-30 | GSE275971 | GEO
Project description:MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease Blood was drawn from two groups of cats: 12 healthy cats and 11 cats suffering from hypertrophic cardiomyopathy. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 23 serum samples were analyzed and the groups were compared
2015-07-22 | E-GEOD-49427 | biostudies-arrayexpress
Project description:BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats. METHODS: Total RNA was extracted from 400 M-BM-5l serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats. RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL cats. CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM. Blood was drawn from two groups of cats: 8 healthy cats and 8 cats suffering from diabetes. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 16 serum samples were analyzed and the groups were compared. Due to technical problems during hybridization (leaking chamber), sample 1_4_B (Serum_diabetic_8) was not included into analysis.
2013-04-11 | E-GEOD-37177 | biostudies-arrayexpress
Project description:BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats. METHODS: Total RNA was extracted from 400 µl serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats. RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL cats. CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM.
2013-04-11 | GSE37177 | GEO
Project description:The aim with this study was to evaluate the miRNA-transcriptome in whole blood in cats with or without pre-clinical HCM. Twelve age, sex and breed matched cats were included. Six cats were Norwegian forest cats and six were domestic mixed breed cats. Each breed represented with three healthy and three preclinical cats. The intention was to evaluate if there were differences in miRNA-profiles between healthy and affected cats, but also to evaluate breed differences and which potential targets the identified miRNAs might have. Bioinformatical pipeline included: bcl2fastq was used to convert sequence files to fastq-format. CutAdapt for adapter and sequence quality trimming, statification and quality evaluation with STAR, FastQC and MultiQC, followed by miRNA-prediction in miRDeep2. Human miRNA-sequences were used as main reference, along with mouse and dog as additional references. Predicted miRNAs were further evaluated for data stratification in DESeq2, followed by differential evaluation analyses based on single or more complex group models (includinig initeraction model). For target prediction IntaRNA was used to identify potential gene transcripts targeted in the feline genome, based on exported feline 3'UTR-sequences from Ensemble. As a comparison human targets were evaluated based on lists in miRDB, since miRNAs are usually conserved between species and the feline genome is less well annotated compared to the human. The results highlighted the importance of considering breed differences when evaluating circulating miRNAs in feline whole blood. This is of high relevance for studies trying to identify miRNAs as potential biomarkers. Also, our results only identified one miRNA differentially expressed between healthy and pre-clinical HCM cats within the Norwegian Forest cats, also highlighting breed differences. One reason for only identifying one miRNA may be that the cats were in pre-clinical state, instead of in congestive heart failure.
2025-08-04 | E-MTAB-12138 | biostudies-arrayexpress
Project description:MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease
2015-07-22 | GSE49427 | GEO
Project description:This study investigates multidrug-resistant Klebsiella pneumoniae KP21-10C using whole genome sequencing and targeted energy metabolomics. Genomic sequencing data were generated to characterize the bacterial genome, and targeted LC-MS/MS metabolomics was performed to quantify energy metabolism-related metabolites under doxycycline monotherapy and cepharanthine hydrochloride plus doxycycline combination treatment.
2026-06-25 | MTBLS14858 | MetaboLights
Project description:Feline infectious peritonitis (FIP) is a fatal disease, if left untreated, caused by feline coronavirus (FCoV). Although the role of the immune system in the pathogenesis of FIP remains incompletely understood, an excessive and harmful immune response appears to be a key factor. In a recent study by the same authors, 18 cats with FIP were successfully cured with oral GS-441524. The present study aimed to analyze the molecular signatures of these treated cats using next-generation RNA-sequencing on full blood samples by highlighting key immune pathways involved in disease progression, treatment response, and recovery. Therefore, samples were analyzed at three stages: untreated (d0), treated with the antiviral drug (days 2, 7, 28), and fully cured (days 168, 252, 365). Additionally, gene expression profiles were compared to those of healthy FCoV-infected control cats (n=12) and uninfected healthy control cats (n=5). Multiple tests with adjusted p-value (adj.p<0.001) were performed. Within the first few days of treatment, massive changes in the RNA signature profile were observed, with approximately 75% of expressed genes significantly differentially regulated between d0 and later time points. Notably, a strong antiviral immune response, which was dominant at the onset of the disease, was significantly downregulated within two days, accompanied by a shift in blood cell composition from monocytes and neutrophils to B cells. Our findings revealed a rapid normalization of the blood RNA signature within the first week of treatment suggesting that elimination of the virus from the blood leads to a rapid down-regulation of the damaging immune response.
2025-09-17 | GSE303159 | GEO
Project description:In this study, we aimed to identify novel serum biomarkers in feline primary cardiomyopathies with congestive heart failure, which can help to understand disease pathogenesis and assist the disease diagnosis, prognosis and management. The study included 15 cats diagnosed with CHF and CM, 5 cats with asymptomatic CM and 15 healthy cats.
2020-07-19 | PXD017761 | Pride
Project description:The purpose of this study was the identification of RNAs contained in the urinary exosome (UExo) from dogs and cats. The quality of total RNA in isolated urinary exosome (UExo)-derived total RNAs obtained from the column-based method (urine 1 mL) was checked by using a Bioanalyzer, and samples from normal renal function (NR) group and kidney disease (KD) group were pooled as one sample for each group. We collected NR dogs (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45). For the next generation sequencing, libraries were prepared according to the manufacturer’s protocols and sequenced using 50-base reads acquired by using a HiSeq 2000 platform. The December 2011 (GRCm38/mm10) mouse (Mus musculus) genome data were used as reference. As a result, we could identify the miRNA from these samples.
2018-12-10 | GSE121156 | GEO