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Series GSE76499 Query DataSets for GSE76499
Status Public on Jun 01, 2016
Title Transcriptomic approaches in the zebrafish model for tuberculosis – insights into host- and pathogen-specific determinants of the innate immune response
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary Both embryonic and adult zebrafish Mycobacterium marinum infection studies have contributed to our knowledge of the development and function of tuberculous granulomas, which are typical for mycobacterial pathogenesis. In this review we discuss how transcriptome profiling studies have helped to characterize this infection process and we include new RNA sequencing (RNA-Seq) data that reveals three main phases in the host response to M. marinum during the early stages of granuloma development in zebrafish embryos and larvae. The late-phase response shares common components with the strong and acute host transcriptome response that has previously been reported for S. typhimurium infection in zebrafish embryos. In contrast, the early/mid-phase response to M. marinum infection, characterized by suppressed pro-inflammatory signaling, is strikingly different from the acute response to S. typhimurium infection. Furthermore, M. marinum infection shows a collective and strongly fluctuating regulation of lipoproteins, while S. typhimurium infection has pronounced effects on amino acid metabolism and glycolysis.
Overall design Embryos were infected at 28 hpf by injecting 250 colony forming units of M. marinum Mma20 in 2%PVP into the caudal vein, or mock-injected with PBS/2%PVP. After injections, embryos were transferred into fresh egg water containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanization and incubated at 28°C. After the incubation period, infected and uninfected groups of 30 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis. Samples were taken at the following timepoints: 2, 4, 6, 8 hpi and 1, 2, 3, 4, 5 dpi.
Contributor(s) Benard EL, Rougeot J, Racz PI, Spaink HP, Meijer AH
Citation(s) 27503359
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Annemarie H. Meijer
Organization name Institute of Biology, Leiden University
Department Animal Sciences and Health
Street address Einsteinweg 55
City Leiden
ZIP/Postal code 2333 CC
Country Netherlands
Platforms (1)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
Samples (72)
GSM2027034 2 hpi uninfected_rep1
GSM2027035 2 hpi uninfected_rep2
GSM2027036 2 hpi uninfected_rep3
BioProject PRJNA307576
SRA SRP068026

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Supplementary file Size Download File type/resource
GSE76499_RAW.tar 9.2 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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