Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

De novo transcriptome assembly and analysis of differential gene expression following lipopolysaccharide challenge in Pelteobagrus fulvidraco

(2018) Qiu-Ning Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis provides insights into the immune responsive pathways and genes in the head kidney of tiger grouper ( Epinephelus fuscoguttatus ) fed with Spatholobus suberectus , Phellodendron amurense , or Eclipta prostrata

(2018) Yan Cai et al.   FISH & SHELLFISH IMMUNOLOGY

Identification of immune-related genes in gill cells of Japanese eels ( Anguilla japonica ) in adaptation to water salinity changes

(2018) Jie Gu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling provides gene resources for understanding gill immune responses in Japanese flounder ( Paralichthys olivaceus ) challenged with Edwardsiella tarda

(2018) Zan Li et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptomic profiling analysis of tilapia ( Oreochromis niloticus) following Streptococcus agalactiae challenge

(2017) Jiajie Zhu et al.   FISH & SHELLFISH IMMUNOLOGY

Deciphering transcriptome profile of the yellow catfish ( Pelteobagrus fulvidraco ) in response to Edwardsiella ictaluri

(2017) Rong Zhu et al.   FISH & SHELLFISH IMMUNOLOGY

Trancriptome profiles of Amur sturgeon spleen in response to Yersinia ruckeri infection

(2017) Shaowu Li et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis reveals temperature-regulated antiviral response in turbot Scophthalmus maximus

(2017) Jian Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling and expression analysis of immune responsive genes in the liver of Golden mahseer ( Tor putitora ) challenged with Aeromonas hydrophila

(2017) Rohit Kumar et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis and discovery of genes involved in immune pathways in large yellow croaker ( Larimichthys crocea ) under high stocking density stress

(2017) Peng Sun et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptomic variation of locally-infected skin of Epinephelus coioides reveals the mucosal immune mechanism against Cryptocaryon irritans

(2017) Yazhou Hu et al.   FISH & SHELLFISH IMMUNOLOGY

Comparative transcriptome analysis of zebrafish ( Danio rerio ) brain and spleen infected with spring viremia of carp virus (SVCV)

(2017) Yeda Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of hybrid tilapia ( Oreochromis spp.) with Streptococcus agalactiae infection identifies Toll-like receptor pathway-mediated induction of NADPH oxidase complex and piscidins as primary immune-related responses

(2017) Chuian-Fu Ken et al.   FISH & SHELLFISH IMMUNOLOGY

More than just antibodies: Protective mechanisms of a mucosal vaccine against fish pathogen Flavobacterium columnare

(2017) Dongdong Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptomic analysis of spleen infected with infectious salmon anemia virus reveals distinct pattern of viral replication on resistant and susceptible Atlantic salmon ( Salmo salar )

(2017) Phillip Dettleff et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling of spleen provides insights into the antiviral mechanism in Schizothorax prenanti after poly (I: C) challenge

(2017) Xiaogang Du et al.   FISH & SHELLFISH IMMUNOLOGY

RNA-Seq transcriptome analysis of the olive flounder ( Paralichthys olivaceus ) kidney response to vaccination with heat-inactivated viral hemorrhagic septicemia virus

(2017) Jee Youn Hwang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome data analysis of grass carp ( Ctenopharyngodon idella ) infected by reovirus provides insights into two immune-related genes

(2017) Zao Dai et al.   FISH & SHELLFISH IMMUNOLOGY

Comparison of grouper infection with two different iridoviruses using transcriptome sequencing and multiple reference species selection

(2017) Chun-Cheng Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling of developing spleen tissue and discovery of immune-related genes in grass carp ( Ctenopharyngodon idella )

(2017) Guoxi Li et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of immune response against Vibrio harveyi infection in orange-spotted grouper ( Epinephelus coioides )

(2017) Shun Maekawa et al.   FISH & SHELLFISH IMMUNOLOGY

Integrated profiling of global metabolomic and transcriptomic responses to viral hemorrhagic septicemia virus infection in olive flounder

(2017) Se-Young Cho et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of yellow catfish ( Pelteobagrus fulvidraco ) liver challenged with polyriboinosinic polyribocytidylic acid (poly I:C)

(2017) Yu Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of the spleen of the darkbarbel catfish Pelteobagrus vachellii in response to Aeromonas hydrophila infection

(2017) Chuanjie Qin et al.   FISH & SHELLFISH IMMUNOLOGY

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

(2017) Santiago J. Carmona et al.   GENOME RESEARCH

Transcriptome Analysis Reveals Increases in Visceral Lipogenesis and Storage and Activation of the Antigen Processing and Presentation Pathway during the Mouth-Opening Stage in Zebrafish Larvae

(2017) Hao Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The flagellar master operonflhDCis a pleiotropic regulator involved in motility and virulence of the fish pathogenYersinia ruckeri

(2017) A.K.S. Jozwick et al.   JOURNAL OF APPLIED MICROBIOLOGY

Characterization of Mycobacterium marinum infections in zebrafish wounds and sinus tracts

(2017) Ling Chen et al.   WOUND REPAIR AND REGENERATION

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

(2017) Emmanouil I. Athanasiadis et al.   Nature Communications

Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study

(2017) Elena Chaves-Pozo et al.   Scientific Reports

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

Advances in the study of nodavirus

(2017) Chean Yeah Yong et al.   PeerJ

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

(2017) Xuehong Song et al.   Scientific Reports

An integrated and comprehensive transcriptome reveals immune-related genes and signal pathways in topmouth culter (Culter alburnus)

(2016) Shuangyong Lei et al.   AQUACULTURE RESEARCH

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

(2016) Mark P. Polinski et al.   BMC GENOMICS

Immunity comes first: The effect of parasite genotypes on adaptive immunity and immunization in three-spined sticklebacks

(2016) David Haase et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Transcriptome profiling of grass carp ( Ctenopharyngodon idellus ) infected with Aeromonas hydrophila

(2016) Ying Yang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of the effect of Vibrio alginolyticus infection on the innate immunity-related TLR5-mediated induction of cytokines in Epinephelus lanceolatus

(2016) Yi-Da Wang et al.   FISH & SHELLFISH IMMUNOLOGY

RNA-Seq revealed the impairment of immune defence of tilapia against the infection of Streptococcus agalactiae with simulated climate warming

(2016) Le Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Understanding the interaction between Betanodavirus and its host for the development of prophylactic measures for viral encephalopathy and retinopathy

(2016) Janina Z. Costa et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome and analysis on the complement and coagulation cascades pathway of large yellow croaker (Larimichthys crocea) to ciliate ectoparasite Cryptocaryon irritans infection

(2016) Fei Yin et al.   FISH & SHELLFISH IMMUNOLOGY

Comprehensive identification and profiling of Nile tilapia (Oreochromis niloticus) microRNAs response to Streptococcus agalactiae infection through high-throughput sequencing

(2016) Bei Wang et al.   FISH & SHELLFISH IMMUNOLOGY

RNA-Seq analysis of immune-relevant genes in Lateolabrax japonicus during Vibrio anguillarum infection

(2016) Chao Zhao et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptomic analysis of koi (Cyprinus carpio) spleen tissue upon cyprinid herpesvirus 3 (CyHV3) infection using next generation sequencing

(2016) Xuezhu Lee et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome signatures in common carp spleen in response to Aeromonas hydrophila infection

(2016) Yanliang Jiang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans

(2016) Panpan Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Characterization of grass carp spleen transcriptome during GCRV infection

(2016) B.H. Xu et al.   GENETICS AND MOLECULAR RESEARCH

RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies

(2016) Paolo Ronza et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Transcriptome analysis of dormant tomonts of the marine fish ectoparasitic ciliate Cryptocaryon irritans under low temperature

(2016) Fei Yin et al.   Parasites & Vectors

Comparative transcriptional profile of the fish parasite Cryptocaryon irritans

(2016) Ze-Quan Mo et al.   Parasites & Vectors

De novo assembly and transcriptome analysis of Atlantic salmon macrophage/dendritic-like TO cells following type I IFN treatment and Salmonid alphavirus subtype-3 infection

(2015) Cheng Xu et al.   BMC GENOMICS

Transcriptome comparative analysis revealed poly(I:C) activated RIG-I/MDA5-mediated signaling pathway in miiuy croaker

(2015) Qing Chu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis revealed positive selection of immune-related genes in tilapia

(2015) Jun Xiao et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish

(2015) Chao Tong et al.   FISH & SHELLFISH IMMUNOLOGY

High-throughput transcriptome analysis of ISAV-infected Atlantic salmon Salmo salar unravels divergent immune responses associated to head-kidney, liver and gills tissues

(2015) Diego Valenzuela-Miranda et al.   FISH & SHELLFISH IMMUNOLOGY

Trancriptomic profiling revealed the signatures of acute immune response in tilapia (Oreochromis niloticus) following Streptococcus iniae challenge

(2015) Jiajie Zhu et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection

(2015) Xiang Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis and microsatellite discovery in the blunt snout bream (Megalobrama amblycephala) after challenge with Aeromonas hydrophila

(2015) Ngoc Tuan Tran et al.   FISH & SHELLFISH IMMUNOLOGY

Piscine reovirus, but not Jaundice Syndrome, was transmissible to Chinook Salmon,Oncorhynchus tshawytscha(Walbaum), Sockeye Salmon,Oncorhynchus nerka(Walbaum), and Atlantic Salmon,Salmo salarL.

(2015) K A Garver et al.   JOURNAL OF FISH DISEASES

Identification of differentially expressed genes of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in response to Tetracapsuloides bryosalmonae (Myxozoa)

(2015) Gokhlesh Kumar et al.   PARASITOLOGY RESEARCH

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

(2015) Quanyuan Wan et al.   Scientific Reports

Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

(2015) Jingqun Ao et al.   PLoS Genetics

RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis

(2015) Diego Robledo et al.   BMC GENOMICS

De Novo Assembly of the Japanese Flounder (Paralichthys olivaceus) Spleen Transcriptome to Identify Putative Genes Involved in Immunity

(2015) Lin Huang et al.   PLoS One

Transcriptome analysis of the effect of Vibrio alginolyticus infection on the innate immunity-related complement pathway in Epinephelus coioides

(2014) Yi-Da Wang et al.   BMC GENOMICS

T cell transcripts and T cell activities in the gills of the teleost fish sea bass (Dicentrarchus labrax)

(2014) N. Nuñez Ortiz et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections

(2014) Ruijia Wang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

A putative serine protease, SpSsp1, from Saprolegnia parasitica is recognised by sera of rainbow trout, Oncorhynchus mykiss

(2014) Kirsty L. Minor et al.   Fungal Biology

RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

(2014) Mijuan Shi et al.   MOLECULAR IMMUNOLOGY

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

RNA-Seq Technology and Its Application in Fish Transcriptomics

(2014) Xi Qian et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Transciptome Analysis of the Gill and Swimbladder of Takifugu rubripes by RNA-Seq

(2014) Jun Cui et al.   PLoS One

RNA-seq Analysis of Early Hepatic Response to Handling and Confinement Stress in Rainbow Trout

(2014) Sixin Liu et al.   PLoS One

RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

(2014) Cristian Gallardo-Escárate et al.   PLoS One

De Novo Characterization of the Spleen Transcriptome of the Large Yellow Croaker (Pseudosciaena crocea) and Analysis of the Immune Relevant Genes and Pathways Involved in the Antiviral Response

(2014) Yinnan Mu et al.   PLoS One

Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates

(2014) David Haase et al.   PLoS One

Transcriptional Responses of Olive Flounder (Paralichthys olivaceus) to Low Temperature

(2014) Jinwei Hu et al.   PLoS One

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

(2014) Ali Ali et al.   Frontiers in Genetics

RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species

(2013) Steve Smith et al.   BMC GENOMICS

Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish

(2013) Ruijia Wang et al.   BMC GENOMICS

Pathogen recognition receptors in channel catfish: III Phylogeny and expression analysis of Toll-like receptors

(2013) Jiaren Zhang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Fate of Tetracapsuloides bryosalmonae (Myxozoa) after infection of brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss

(2013) G Kumar et al.   DISEASES OF AQUATIC ORGANISMS

Analysis of Stress-Responsive Transcriptome in the Intestine of Asian Seabass (Lates calcarifer) using RNA-Seq

(2013) J. H. Xia et al.   DNA RESEARCH

Early mucosal responses in blue catfish (Ictalurus furcatus) skin to Aeromonas hydrophila infection

(2013) Chao Li et al.   FISH & SHELLFISH IMMUNOLOGY

Genomic analysis of the host response to nervous necrosis virus in Atlantic cod (Gadus morhua) brain

(2013) Aleksei Krasnov et al.   MOLECULAR IMMUNOLOGY

Basal polarization of the mucosal compartment in Flavobacterium columnare susceptible and resistant channel catfish (Ictalurus punctatus)

(2013) Eric Peatman et al.   MOLECULAR IMMUNOLOGY

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

De Novo Assembly of Mud Loach (Misgurnus anguillicaudatus) Skin Transcriptome to Identify Putative Genes Involved in Immunity and Epidermal Mucus Secretion

(2013) Yong Long et al.   PLoS One

Short-Term Feed Deprivation Alters Immune Status of Surface Mucosa in Channel Catfish (Ictalurus punctatus)

(2013) Lisa Liu et al.   PLoS One

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

(2013) Rays H. Y. Jiang et al.   PLoS Genetics

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish

(2012) Dahai Yang et al.   BMC GENOMICS

Transcriptome characterization and gene expression of Epinephelus spp in endoplasmic reticulum stress-related pathway during betanodavirus infection in vitro

(2012) Ming-Wei Lu et al.   BMC GENOMICS

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pathogen recognition receptors in channel catfish: II. Identification, phylogeny and expression of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs)

(2012) K.V. Rajendran et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection

(2012) Fanyue Sun et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Putative roles for a rhamnose binding lectin in Flavobacterium columnare pathogenesis in channel catfish Ictalurus punctatus

(2012) Benjamin H. Beck et al.   FISH & SHELLFISH IMMUNOLOGY

RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

(2012) Chao Li et al.   FISH & SHELLFISH IMMUNOLOGY

Sequencing of the first ayu (Plecoglossus altivelis) macrophage transcriptome and microarray development for investigation the effect of LECT2 on macrophages

(2012) Xin-Jiang Lu et al.   FISH & SHELLFISH IMMUNOLOGY

Immune system and immune responses in fish and their role in comparative immunity study: A model for higher organisms

(2012) Pradipta R. Rauta et al.   IMMUNOLOGY LETTERS

Koi Herpes Virus: A Review and Risk Assessment of Indian Aquaculture

(2012) Gaurav Rathore et al.   Indian Journal of Virology

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Expression of the Infectious Salmon Anemia Virus Receptor on Atlantic Salmon Endothelial Cells Correlates with the Cell Tropism of the Virus

(2012) M. Aamelfot et al.   JOURNAL OF VIROLOGY

Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum

(2012) E. Sarropoulou et al.   MARINE BIOTECHNOLOGY

Applications for next-generation sequencing in fish ecotoxicogenomics

(2012) Alvine C. Mehinto et al.   Frontiers in Genetics

Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus

(2011) Youhua Huang et al.   BMC GENOMICS

Pathogen recognition receptors in channel catfish: I. Identification, phylogeny and expression of NOD-like receptors

(2011) K.V. Rajendran et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

RNA-Seq Reveals an Integrated Immune Response in Nucleated Erythrocytes

(2011) Davinia Morera et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection

(2010) Yinnan Mu et al.   BMC GENOMICS

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

(2010) Li-xin Xiang et al.   BMC GENOMICS

Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

(2010) Anita Ordas et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos

(2010) Oliver W. Stockhammer et al.   MOLECULAR IMMUNOLOGY

Heart and Skeletal Muscle Inflammation of Farmed Salmon Is Associated with Infection with a Novel Reovirus

(2010) Gustavo Palacios et al.   PLoS One

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The use of immunostimulating herbs in fish. An overview of research

(2009) Jeney Galina et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Comparison of the susceptibility of brown trout (Salmo trutta) and four rainbow trout (Oncorhynchus mykiss) strains to the myxozoan Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD)

(2009) Daniel S. Grabner et al.   VETERINARY PARASITOLOGY

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Small non-coding RNAs in animal development

(2008) Giovanni Stefani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY