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Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq]

ABSTRACT: We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum

ORGANISM(S): Danio rerio

PROVIDER: GSE44351 | GEO | 2013/08/01

SECONDARY ACCESSION(S): PRJNA189536

REPOSITORIES: GEO

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Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq]

Project description:We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum This RNA deep sequencing study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

2013-08-01 | E-GEOD-44351 | biostudies-arrayexpress

Gene expression profiling of zebrafish embryos at 5 days post fertilization [Agilent Arrays]

Project description:We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes. This microarray study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. The samples were analyzed in a technical duplicate using a dye swap experiment in order to check for dye bias.

2013-08-01 | E-GEOD-44226 | biostudies-arrayexpress

Gene expression profiling of zebrafish embryos at 5 days post fertilization

Project description:We use the zebrafish embryo model to study the innate immune response against Mycobacterium marinum. Therefore, we injected M. marinum into the yolk at the 64 cell stage and took samples at 5 days post injection. This deep sequence study was designed to determine the gene expression profile by Mycobacterium marinum infection. RNA was isolated from embryos at 5 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (64 cell stage) with 40 CFU of Mycobacterium marinum E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. At 5 days post injection 50 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

2014-12-11 | E-GEOD-57792 | biostudies-arrayexpress

Gene expression profiling of zebrafish embryos at 5 days post fertilization

2014-12-11 | GSE57792 | GEO

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

Project description: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.

2013-09-16 | E-GEOD-45409 | biostudies-arrayexpress

Gene expression profiling of the Tlr2 mutant of zebrafish embryos at 4 days post infection of M. marinum

Project description:We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection.

2018-01-01 | GSE102766 | GEO

Gene expression profiling of zebrafish embryos at 5 days post fertilization [Agilent Arrays]

2013-08-01 | GSE44226 | GEO

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

2013-09-16 | GSE45409 | GEO

Zebrafish response to Mycobacterium marinum infection (Affymetrix series)

Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum, mock-infected, or uninfected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Keywords: host response to infection

2008-01-01 | GSE8327 | GEO

Zebrafish response to Mycobacterium marinum infection (Compugen series)

Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum or mock-infected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Keywords: host response to infection

2008-01-01 | GSE8846 | GEO

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