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Oryzias sakaizumii

ABSTRACT: Experimental Evolution of a Neo-Sex Chromosome in Medaka

PROVIDER: PRJDB12965 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR344879_1.fastq.gz	Fastqsanger.gz
	DRR344879_2.fastq.gz	Fastqsanger.gz
	DRR344880_1.fastq.gz	Fastqsanger.gz
	DRR344880_2.fastq.gz	Fastqsanger.gz
	DRR344881_1.fastq.gz	Fastqsanger.gz

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Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

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Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

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H3K27ac and H3K4me3 ChIP-seq in Oryzias latipes

Project description:Here we analyze key epigenetic marks from medaka (O. latipes) during the vertebrate phylotypic period (stage 24).

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H3K27ac and H3K4me3 ChIP-seq in Oryzias latipes

Project description:Here we analyze key epigenetic marks from medaka (O. latipes) during the vertebrate phylotypic period (stage 24). Chromatin immuno-precipitation with histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation antibodies.

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Project description:Mus minutoides neo-sex chromosomes evolution

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Variation of the genomic expression pattern after exposed to 17beta-estradiol in Japanese medaka (Oryzias latipes)

Project description:We assess gene expression patterns upon 17beta-estradiol (E2) exposure to Japanese medaka (Oryzias latipes) in order to appere the E2 effects using DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, fish were sacrificed and mRNA was extracted for gene expression analysis. In an effort to link gene expression changes to effects on higher levels of biological organization, sex characteristics, gonadal histology, GSI, and egg production and fertility were examined. In microarray experiments, the correlation factors between the controls were from 0.91 to 1.00 among control samples. We observed highly induced O. latipes Gene Indices (OLGI) related to egg-yolk protein such as vitellogenin and L-SF precursor etc., which were significantly affected in a concentration-dependent manner by E2 exposure. To clarify the function of expressed genes by E2 treatments, we selected statistically expressed genes from the microarray experiments. We found 190 genes and 72 genes which were statistically expressed in E2 treatment as induced and repressed genes, respectively. In the induced gene list, there were characteristic induced-genes in the categories of lipid metabolism, stress (oxidative stress, DNA and protein damage), and apoptosis with MAPK pathway. On the other hands, there were characteristic repressed genes in the categories of heat shock protein. Our result may suggest that gene expressions in yolk medaka is able to be used for detection of E2 effect by DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration and time-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, three independent samples (one sample contained thirty whole medakas) were sacrificed and mRNA was extracted for gene expression analysis.

2010-05-01 | E-GEOD-17633 | biostudies-arrayexpress

Identification and expression profiling of microRNAs in brain, liver and gonads of marine medaka (Oryzias melastigma) by Illumina small RNA Sequencing

Project description:We performed miRNA transcriptome analysis of mature medaka tissues using high-throughput next generation sequencing technology. The small RNA libraries were contructed from brain, liver and gonads in mature male and female medaka and a total of more than 128 million sequencing reads were generated from the six small RNA libraries. By comparison to known miRNA database, a total of 223 known miRNA types were identified with more than 50% expressed in brain. The expression profiling showed that almost half of the miRNAs are tissue-specific, with only 55 miRNA types from 34 families common to all tissues. A small number of miRNAs are also gender-specific. The experimental validation was performed for five represented miRNA candidates and four of them are confirmed.

2014-07-01 | GSE42696 | GEO

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