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Oryzias latipes

ABSTRACT: UPA-Seq using brain of medaka fish

PROVIDER: PRJDB7434 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR150892.fastq.gz	Fastqsanger.gz
	DRR150893.fastq.gz	Fastqsanger.gz
	DRR150894.fastq.gz	Fastqsanger.gz
	DRR150895.fastq.gz	Fastqsanger.gz
	DRR150896.fastq.gz	Fastqsanger.gz

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Seasonal changes of gene expression of eyes in Medaka fish (Oryzias latipes)

Project description:To examine the seasonal adaptation, we compared the gene expression of eyes between SL (short-day and low-temperature conditions: 10 h light/14 h dark and 8 °C) and LD (long-day and warm-temperature conditions: 14 h light/10 h dark and 26 °C) conditions in Medaka fish (Oryzias latipes).

2017-09-01 | GSE94258 | GEO

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).

2014-03-25 | GSE46351 | GEO

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.

2014-03-25 | E-GEOD-46351 | biostudies-arrayexpress

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

Project description:Alkalinity stress is considered to be one of the major stressors for fish in saline-alkali water. Thus, it is of great significance from both aquaculture and physiological viewpoint to understand the molecular genetic response of aquatic organisms to alkalinity stress. The objective of this study is to determine genome-wide gene expression profiles to better understand the physiology response of medaka (Oryzias latipes) to high carbonate alkalinity stress. In lab-based cultures, adult fish were exposed to freshwater and high carbonate alkalinity water .We designed a microarray containing 26429 oligonucleotides and describe our experimental results for measuring gene expression changes in the gill of carbonate alkalinity stress exposed fish.

2014-01-24 | GSE27298 | GEO

Oryzias latipes

Project description:Seasonal changes of gene expression of eyes in Medaka fish (Oryzias latipes)

| PRJNA369208 | ENA

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

2014-01-24 | E-GEOD-27298 | biostudies-arrayexpress

RNA-seq in Oryzias latipes at stage 24

Project description:Sequencing of the total RNA of whole embryos of medaka at developmental stage 24. 2 Samples, 60 embryos per sample, were sequenced using Illumina HiSeq 2000.

2014-03-25 | E-GEOD-46484 | biostudies-arrayexpress

RNA-seq of tissue panel samples from zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss)

Project description:The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss). Tissue types included liver, skin, muscle, heart, gut, gill, eye, brain for all three species, with additionally pyloric caeca, kidney, head kidney, and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired‐end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125‐bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.

2020-04-30 | E-MTAB-8959 | biostudies-arrayexpress

Oryzias latipes strain:Cab

Project description:Mutations in a non-visual opsin alters gene expression in the brain of medaka fish

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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

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