E-GEOD-45409 - MicroRNA-146 function in the innate immune response of zebrafish embryos to Salmonella typhimurium infection [miRNA profile]

Released on 16 September 2013, last updated on 2 June 2014
Danio rerio
Samples (18)
Array (1)
Protocols (7)
This study reports on infection-inducible miRNAs in zebrafish. Using a custom-designed microarray platform for miRNA expression we found that miRNAs of the miR-21, miR-29, and miR-146 families were commonly induced by infection of zebrafish embryos with Salmonella typhimurium and by infection of adult fish with Mycobacterium marinum. A custom-designed Agilent zebrafish 8x15k miRNA platform was used to profile miRNA expression in zebrafish embryos infected with Salmonella typhimurium strain SL1027 and adult zebrafish infected with Mycobacterium marinum strain Mma20 . The 15k design contained a duplicate of 7604 probes of 60-oligonucleotide length. The probes consisted of 2x22 nucleotide sequences antisense to mature miRNAs separated by a spacer of 8 nucleotides (CGATCTTT) and with a second spacer with the same sequence at the end. From 7604 probes 546 were designed for left (5') and right (3') arms of the hairpins of zebrafish miRNAs known in miRBase, while the remainder 7058 probes corresponded to predicted hairpin structures in the zebrafish genome that might include additional miRNAs but were not considered in this study. Zebrafish embryos were infected at 28 hours post fertilization (hpf) by injecting 200-250 colony forming units of Salmonella typhimurium into the caudal vein and miRNA profiles of infected embryos were compared to control embryos injected with PBS (phosphate buffered saline) at 8 hours post-infection (hpi; 3 biological replicates and 2 technical replicates per each sample). Adult zebrafish were infected with 10000 colony forming units of Mycobacterium marinum and miRNA profiles were compared to PBS-injected control fish at 6 days post infection (dpi; 3 biological replicates). For dual color hybridization of the Agilent chips miRNA samples from infected zebrafish were labeled with Hy3 and samples from control fish were labeled with Hy5.
Experiment type
transcription profiling by array 
Annemarie H. Meijer <a.h.meijer@biology.leidenuniv.nl>, Anita Ordas, Annemarie H Meijer, Herman P Spaink, Matyas Mink, Valesca Lindenberg, Zakia Kanwal
Investigation descriptionE-GEOD-45409.idf.txt
Sample and data relationshipE-GEOD-45409.sdrf.txt
Raw data (1)E-GEOD-45409.raw.1.zip
Processed data (1)E-GEOD-45409.processed.1.zip
Array designA-GEOD-15403.adf.txt