Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 12
Release date: Sep 1 2014
Last update date: Jul 26 2018
Access: Public
Genes: MPEG1, mpeg1.2, mpeg1.1, MYD88
Taxon: Mycobacterium marinum, Salmonella enterica subsp. enterica serovar Typhimurium, Danio rerio
Dataset link Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish

Experimental Protocol


Embryos were injected at the one cell stage with a morpholino targeting mpeg1, or with the standard control morpholino from GeneTools, or with a morpholino targeting ptpn6 (Kanwal et al., 2013, J. Immunol 190:1631-45) for comparison. Subsequently, at 24 hours post fertilisation (hpf) the morphants and their controls were manually dechorionated at 24 hpf and at 28 hpf they were infected by injecting 200 colony forming units of M. marinum Mma20 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 melanisation and incubated for 4 days at 28°C. After the incubation period, infected and uninfected morphants, mutants and their controls were imaged and groups of 30 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.

Repositories


GEO

GSE54885

ArrayExpress

E-GEOD-54885

ENA

SRP037583

BioProject

PRJNA237966

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Contact


Annemarie Meijer
Annemarie H. Meijer