Feline microRNA transcriptome in whole blood in 6 healthy cats and in 6 cats with preclinical hypertrophic cardiomyopathy
type: Dataset
description: Aim to characterize differentially expressed miRNAS between healthy Norwegian Forest cats and healthy Domestic Shorthair cats, and to compare with cats with hypertropic cardiomyopathy (HCM) Six neutered healthy cats, three male domestic cats (DOM) and one male and two female Norwegian Forest (NF) cats were included. Each healthy cat was matched (breed, sex, age, body-weight and body condition score) with a cat with HCM. The dataset includes the miRDeep2 report, rawcounts miRNAs, differentially expressed miRNAs for contrasts compared using DESeq2, human and feline target genes producing messenger RNA (mRNA) and gene ontology analysis (GO) for these 12 cats. Whole blood was collected in PAXgene blood RNA System frozen and stored in -20 °C until date of RNA-extraction for a median storage time of 177 days. Total RNA was extracted. Samples with an RNA integrity number (RIN)-value of 7.7 or higher were included in the study. Libraries were prepared and quantified and normalized prior sequencing. Paired-end sequencing data was generated. Bioformatic data processing and count genertion of known and novel miRNAs in cats were identified using miRDeep2. Mature miRNA and hairpin sequences were downloaded from miRBase with human as main reference, an mouse and dog assigned as close relatives. Main reference miRNAs identified in the dataset were classified as predicted known miRNAs, and miRNAs previously not described in the main reference were classified as novel miRNAs by miRDeep2. Only novel miRNAs with a miRDeep2 score of >5.0 was included in the count-file generated for subsequent differently expressed (DE)-analyses. Identification of DE miRNAs were performed in DESeq2. Number of variables 6: breed, age, sex, body-weight, body condition score, healthy or hypertrophic cardiomyopathy. The compiled files gives an overview of the data set. Compiled Excel file “miRDeep2_counts_DEsignmiRNAcontrasts_compiled” is a compiled file with the miRDeep2 report, raw counts of miRNAs and th…
conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
conditions of access: info:eu-repo/semantics/openAccess
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Sofia Hanås
creator: Julie Lorent
  type: Person
  affiliation: Science for Life Laboratory
  family name: Lorent
  given name: Julie
creator: Åsa Ohlsson
  type: Person
  affiliation: Swedish University of Agricultural Sciences
  family name: Ohlsson
  given name: Åsa
date modified: 2022-01-07
date published: 2022-01-07
funding: Felina cirkulerande biomarkörer för hjärtsjukdom hos katt
  type: Grant
  identifier: Projektnummer N2013-0025, P2014-0014, P2015-0004 och P2016-0003.
  funder: Agria and the Swedish Kennel Club’s research fund
funding: Cirkulerande biomarkörer hos katter med hjärtsjukdom
  type: Grant
  funder: Sveland Research Fund
funding: Cirkulerande biomarkörer hos katter med och utan hjärtsjukdom
  type: Grant
  funder: SLU Companion Animals Research Fund
funding: Cirkulerande biomarkörer hos katter med och utan hjärtsjukdom
  type: Grant
  funder: Foundation Strömsholms Djursjukvård
language: English
is part of: https://doi.org/10.5878/swmf-jk04
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: Genetics and Genomics
  type: DefinedTerm
  term code: 10609
keywords: Basic Medicine
  type: DefinedTerm
  term code: 301
keywords: Medical Genetics and Genomics
  type: DefinedTerm
  description: Including: Gene Therapy
  term code: 30107
keywords: Veterinary Science
  type: DefinedTerm
  term code: 403
keywords: Norwegian Forest cat
keywords: breed
keywords: microRNA
keywords: hypertrophic cardiomyopathy
keywords: Domestic cat
publisher: Swedish University of Agricultural Sciences
size: QuantitativeValue
  unit text: cases
  value: 12
size: QuantitativeValue
  unit text: variables
  value: 6
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