Project description:Comparison of transcriptome of 24 hours post fertilisation wild-type zebrafish embryos and that of embryos depleted of Kcng4b using anti-Kcng4b CRISPR (5’- GGCAGAGAAGGAATTCAGCA-3’, gRNA target site in exon 3) and splice site-blocking MO (5′-TGCATTCGCCCTGTAAAAGAACAAA-3′) targeting kcng4b intron 2-exon 3 (I2E3) junction.
Project description:In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).
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.
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.