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Title: Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection      
dateReleased:
10-25-2010
description:
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. Comparison of tag-based sequencing (DGE or Tag-Seq) with full transcript sequencing (RNA-Seq) showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A slightly 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 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. Zebrafish embryos were infected with Salmonella typhimurium (strain SL1027) by microinjection of DsRED-labeled bacteria into the caudal vein close to the urogenital opening after the onset of blood circulation (27 hpf). An equal volume of PBS was injected in the control group. RNA samples were collected at 8 hours post infection (hpi) and samples from triplicate infection experiments were pooled. DGE libraries from the RNA pools (1 μg) of Salmonella-infected and control embryos were prepared using the DGE:Tag Profiling for NlaIII Sample Prep kit from Illumina as previously described (Hegedus et al., 2009). The libraries were sequenced in duplicate using 2 (Control 1; Salmonella infected 1) and 3 pmol (Control 2; Salmonella infected 2) of cDNA. Sequencing was performed using the Illumina Genome Analyzer II System (BaseClear B.V., Leiden, The Netherlands) according to the manufacturer’s protocols. Image analysis, base calling, extraction of 17 bp tags and tag counting were performed using the Illumina pipeline. Tag counts from duplicate libraries were merged in silico.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-22472
refinement:
raw
alternateIdentifiers:
22472
keywords:
functional genomics
dateModified:
11-06-2012
availability:
available
types:
gene expression
name:
Danio rerio
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22472/E-GEOD-22472.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22472/E-GEOD-22472.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22472
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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