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RNA-Seq of zebrafish whole-eye comparing wild-type and mab21l1 c.107delA p.(Lys36Argfs*7) embryos at 5 days post fertilization

ABSTRACT: RNA-Seq of zebrafish whole-eye comparing wild-type and mab21l1 c.107delA p.(Lys36Argfs*7) embryos at 5 days post fertilization

PROVIDER: PRJEB42852 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5236191_1.fastq.gz	Fastqsanger.gz
	ERR5236191_2.fastq.gz	Fastqsanger.gz
	ERR5236192_1.fastq.gz	Fastqsanger.gz
	ERR5236192_2.fastq.gz	Fastqsanger.gz
	ERR5236193_1.fastq.gz	Fastqsanger.gz

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RNA-Seq of zebrafish whole-eye comparing wild-type and mab21l1 c.107delA p.(Lys36Argfs*7) embryos at 5 days post fertilization

Project description:Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore, we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA-seq on zebrafish whole eyes which were dissected out at 5 days post fertilization. Three biological replicates per genotype (wild-type or homozygous mab21l1-c.107delA) were collected, with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA-Sequencing procedure.

2022-01-26 | E-MTAB-10068 | biostudies-arrayexpress

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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.

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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.

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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.

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