Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome bisulfite sequencing of infectious spleen and kidney necrosis virus

ABSTRACT: To obtain the site-by-site methylation landscape of the infectious spleen and kidney necrosis virus (ISKNV) genome, whole-genome bisulfite sequencing (WGBS) was performed on an ISKNV strain from 3 duplicate samples.

ORGANISM(S): Infectious spleen and kidney necrosis virus

PROVIDER: GSE241500 | GEO | 2023/08/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Infectious spleen and kidney necrosis virus

Project description:Infectious spleen and kidney necrosis virus Genome sequencing and assembly

| PRJNA528806 | ENA

Transcription profiling by array of Atlantic salmon head kidney cells infected with infectious pancreatic necrosis virus

Project description:Infectious pancreatic necrosis (IPN) is a serious viral disease that causes significant economic losses in salmon aquaculture. To characterize the host-pathogen relationship in IPN, we analysed transcriptional profiles of salmon head kidney (SHK-1) cells infected with infectious pancreatic necrosis virus (IPNV) at three timepoints over six days (at 1, 3 & 6 days post infection. The transcriptome was investigated using the TRAITS / SGP 16950-feature Atlantic salmon cDNA microarray, which is enriched for genes with functions related to the immune response.

2011-01-01 | E-TABM-1000 | biostudies-arrayexpress

Infectious Pancreatic Necrosis Virus in Scotland

Project description:Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

| PRJEB28749 | ENA

Whole-genome bisulfite sequencing of Mandarin fish ranavirus

Project description:To characterize the site-specific methylation landscape of the Mandarin fish ranavirus (MRV) genome, whole-genome bisulfite sequencing (WGBS) was conducted on an isolated MRV strain.

2024-04-02 | GSE262554 | GEO

Transcription profiling by array of response of rainbow trout to an Infectious hematopoietic necrosis virus secondary nasal vaccination

Project description:Infectious hematopoietic necrosis virus (IHNV) is a virus of the genus Novirhabdovirus and the causative agent of infectious hematopoietic necrosis (IHN), one of the most serious threats to salmonid fishes. IHN outbreaks can cause more than 80% mortality rates in certain cases. Studying the transcriptional responses to the secondary immunization with a live attenuated IHNV vaccine will help us understand how fish previously immunized respond when they encounter again the same pathogen and how effective this type of vaccination is.This experiment was aimed at understanding the transcriptomic response of rainbow trout to an IHNV secondary nasal vaccination.

2022-02-18 | E-MTAB-4788 | biostudies-arrayexpress

Gene expression profile after oral vaccination against infectious pancreatic necrosis virus (IPNV)

Project description:Oral immunization of trout against infectious pancreatic necrosis virus (IPNV) have been recently reported by using a DNA vector coding the viral capsid VP2 gene encapsulated in alginate microspheres. We report here an study of the transcripts in head kidney and pyloric ceca 7 days after oral vaccination of rainbow trout by using a newly designed rainbow trout 60-mer oligo microarray focused in their immune-related genes.

2012-07-19 | GSE31591 | GEO

Skin immune response of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus

Project description:Rainbow trout (Oncorhynchus mykiss) is one of the economically important cold-water fish cultivated in the world. The outbreak of infectious hematopoietic necrosis (IHN) seriously restricted the development of rainbow trout farming industry and caused huge economic losses. Fish skin is the largest mucosal immune organ, providing the first line of defense against pathogen invasion. However, the immune mechanisms associated with fish skin remain unclear. To systematically identify skin mucosal immune genes induced by infectious hematopoietic necrosis virus (IHNV) infection, trout transcriptome profiles following IHNV challenge were examined. Transcriptome analysis identified 6905 differentially expressed genes (DEGs) and revealed numerous immune-related DEGs involved in cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway, and the expression of these DEGs was significantly up-regulated in T48Skm group, including NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1, and HSP90A1. Additionally, highly interactive DEGs network involving immune-related terms and pathways was shown using protein-protein interaction network. The expression patterns of 12 DEGs were further verified by quantitative real-time PCR, which confirmed the reproducibility and reliability of transcriptome sequencing data. These findings expand our understanding of the innate immune system of rainbow trout skin infected with IHNV, and lay a foundation for further studies of the immune molecular mechanism and disease resistance breeding.

2024-03-11 | GSE252328 | GEO

Bisulfite sequencing of medaka PGCs methylomes

Project description:Medaka PGCs methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

2019-12-25 | GSE130002 | GEO

Bisulfite sequencing of medaka sperm methylomes

Project description:Medaka sperm methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

2019-04-23 | GSE128797 | GEO

Methylated DNA is over-represented in whole-genome bisulfite sequencing data

Project description:The development of whole-genome bisulfite sequencing (WGBS) has led to a number of exciting discoveries about how genomes utilize DNA methylation and has led to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently excelled to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of methylated DNA from WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. MethylC-Seq of Arabidopsis thaliana

2014-09-11 | E-GEOD-58217 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data