PUBLICATION

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

Authors
Ordas, A., Hegedus, Z., Henkel, C.V., Stockhammer, O.W., Butler, D., Jansen, H.J., Racz, P., Mink, M., Spaink, H.P., and Meijer, A.H.
ID
ZDB-PUB-100910-32
Date
2011
Source
Fish & shellfish immunology   31(5): 716-24 (Journal)
Registered Authors
Meijer, Annemarie H., Spaink, Herman P., Stockhammer, Oliver W.
Keywords
Zebrafish embryo, Innate immunity, Salmonella typhimurium, Tag-Seq, RNA-Seq
Datasets
GEO:GSE22472
MeSH Terms
  • Animals
  • Embryo, Nonmammalian/immunology
  • Fish Diseases/immunology*
  • High-Throughput Nucleotide Sequencing*
  • Host-Pathogen Interactions/genetics
  • Immunity, Innate/genetics*
  • Molecular Sequence Annotation
  • Reproducibility of Results
  • Salmonella Infections, Animal/immunology*
  • Transcriptome*
  • Zebrafish/genetics*
  • Zebrafish/immunology*
PubMed
20816807 Full text @ Fish Shellfish Immunol.
Abstract
Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. We obtained 10 million sequence reads from control and Salmonella-infected zebrafish embryos using a tag-based sequencing method (DGE or Tag-Seq) and 15 million reads using whole transcript sequencing (RNA-Seq), which respectively mapped to circa 65% and 85% of 28716 known Ensembl transcripts. Both sequencing methods showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A lower overlap of 165 transcripts was observed with previous microarray data. Based on the combined sequencing-based and microarray-based transcriptome data we compiled an annotated reference set of infection-responsive genes in zebrafish embryos, encoding transcription factors, signal transduction proteins, cytokines and chemokines, complement factors, proteins involved in apoptosis and proteolysis, proteins with anti-microbial activities, as well as many known or novel proteins not previously linked to the immune response. Furthermore, by comparison of the deep sequencing data of S. typhimurium infection in zebrafish embryos with previous deep sequencing data of Mycobacterium marinum infection in adult zebrafish we derived a common set of infection-responsive genes. This gene set consists of known and putative innate host defense genes that are expressed both in the absence and presence of a fully developed adaptive immune system and that provide a valuable reference for future studies of host-pathogen interactions using zebrafish infection models.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping