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

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.

ORGANISM(S): Danio rerio

PROVIDER: GSE44226 | GEO | 2013/08/01

SECONDARY ACCESSION(S): PRJNA189203

REPOSITORIES: GEO

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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 [Illumina RNA-Seq]

2013-08-01 | GSE44351 | GEO

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

Chromosomal integrity of human preimplantation embryos at different days post fertilization.

Project description:IntroductionIn order to investigate the dynamics of genomic alterations that occur at different developmental stages in vitro, we examined the chromosome content of human preimplantation embryos by molecular-cytogenetic techniques at the single-cell level, up to 13 days post fertilization.MethodsThe embryos were genetically analyzed several times during their development in culture; each embryo was first analyzed by FISH at 'Day 3' post fertilization, than during its growth in vitro and the third analysis was performed at development arrest, then the entire blastocyst was analyzed by comparative genomic hybridization (CGH/aCGH).ResultsWe found that while on 'Day 3' only 31% of the embryos were detected as normal, on 'Day 5-6', 44% of the embryos were classified as normal and on 'Day 7', 57% were normal. On 'Days 8-13', 52% of the embryos were classified as chromosomally normal. One third of the embryos that were chromosomally abnormal on 'Day 3', were found to be normal at development arrest point.DiscussionThese dynamic changes that occur at early developmental stages suggest that testing a single blastomere at 'Day 3' post fertilization for PGD might inaccurately reflect the embryo ploidy and increase the risk of false aneuploidy diagnosis. Alternatively, blastocyst stage diagnosis may be more appropriate.

| S-EPMC3663967 | biostudies-literature

Nile tilapia (Oreochromis niloticus) gene expression profiling in males and females at early embryonic development (2, 5 and 9 days post fertilization )

2014-11-01 | GSE50974 | GEO

Nile tilapia (Oreochromis niloticus) gene expression profiling in males and females at early embryonic development (2, 5 and 9 days post fertilization )

Project description:Commercial production of tilapia relies on monosex cultures of males, which so far proved difficult to maintain in large scale production facilities. Thus, a better understanding of the genetic architecture of the complex trait of sex determination in tilapia is needed.We aimed to detect genes that were differentially expressed by gender at early embryonic development. Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively. Pools of all-female and all-male embryos at 2, 5 and 9 days post fertilization were used for custom Agilent eArray. 56 pool samples of Nile tilapia full siblings groups (female or male) at day 2, 5 or 9 post fertilization were subjected to total RNA extraction from whole embryo tissues and hybridized to the custom Agilent array. Each sample was yielded from different cross of artificial fertilization: six dams X five sires. The resulting gender were known based on the sire, sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively.

2014-11-01 | E-GEOD-50974 | biostudies-arrayexpress

Gene expression profiling of zebrafish embryos at 5 days post fertilization

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-08-01 | GSE44352 | GEO

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.

2014-12-11 | GSE57792 | GEO

Gene Expression Profiling of Single Embryos, Significant Effects of In Vitro Maturation, Fertilization and Culture

Project description:In vitro production (IVP) has been shown to affect embryonic gene expression and often result in large offspring syndrome (LOS) in cattle and sheep. To dissect the effects of in vitro maturation, fertilization and culture, we compared the expression profiles of single bovine blastocysts generated by: 1) in vitro maturation, fertilization and culture (IVF); 2) in vivo maturation, fertilization and in vitro culture (IVD); and 3) in vivo maturation, fertilization and development (AI). To conduct expression profiling, total RNA was isolated from individual embryos, linearly amplified and hybridized to a custom bovine cDNA microarray containing approximately 6,300 unique genes. There were 306, 367 and 200 genes differentially expressed between the AI and IVD, IVF and IVD and AI and IVF comparisons, respectively. Interestingly, 44 differentially expressed genes were identified between the AI embryos and both the IVF and IVD embryos, making these potential candidates for LOS. There were 60 genes differentially expressed between the IVF embryos and the AI and IVD embryos. The Gene Ontology category “RNA processing” was over-represented among the genes that were down-regulated in the IVF embryos, indicating an effect of in vitro oocyte maturation/fertilization on embryonic gene expression. A culture effect on the expression of genes involved in translation was also observed by the comparison of AI to IVD embryos. Keywords: developmental condition

2008-05-05 | GSE8807 | GEO

AB* zebrafish embryos exposed to 1 ng/mL TCDD from 1d to 5d post-fertilization.

Project description:Transcriptomic profiling of the response to dioxin in developing zebrafish embryos, at 24, 48, 72, 96, and 120 h post-fertilization. The goal was to elucidate mechanisms by which dioxin causes toxicity in zebrafish; this dose was previously shown to induce teratogenesis.

2010-03-01 | GSE15410 | GEO

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