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Series GSE39274 Query DataSets for GSE39274
Status Public on Dec 10, 2012
Title Pathogen recognition and activation of the innate immune response in zebrafish: MyD88 mutants
Organism Danio rerio
Experiment type Expression profiling by array
Summary MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Salmonella typhimurium and Edwardsiella tarda to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. The data derived from these microarray experiments confirms the vital role of MyD88 in pathogen recognition and provides many leads for further research.
 
Overall design This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Salmonella typhimurium and Edwardsiella tarda. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Homozygous mutants injected with PBS 8 hours post infection (hpi), (2) wildtype siblings injected with PBS 8hpi, (3) S. typhimurium-infected homozygous mutants 8hpi, (4) S. typhimurium-infected wildtype siblings 8hpi, (5) Homozygous mutants injected with PBS 8 hours post infection (hpi) (E.tarda control), (6) wildtype siblings injected with PBS 8hpi (E. tarda control), (7) E. tarda-infected homozygous mutants 8hpi, (8) E. tarda-infected wildtype siblings 8hpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027 or E. Tarda FL-F60, or were mock-injected with buffer as a control. After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28°C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.
 
Contributor(s) van der Vaart M, van Soest JJ, Spaink HP, Meijer AH
Citation(s) 23471913
Submission date Jul 11, 2012
Last update date Jun 04, 2013
Contact name Michiel van der Vaart
Organization name University of Leiden
Department IBL
Lab Molecular cell biology
Street address Einsteinweg 55
City Leiden
ZIP/Postal code 2333 CC
Country Netherlands
 
Platforms (1)
GPL10042 LU/IBL_D.rerio_Agilent_44k_021626
Samples (24)
GSM959593 Biological replicate 1 of 3: mutant embryos PBS control for S.typhimurium
GSM959594 Biological replicate 2 of 3: mutant embryos PBS control for S.typhimurium
GSM959595 Biological replicate 3 of 3: mutant embryos PBS control for S.typhimurium
Relations
BioProject PRJNA170449

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39274_RAW.tar 347.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file
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