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.
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.
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.
Project description:During development, the inherited DNA methylation patterns from the parental gametes needs to be remodeled into a state compatible with embryonic pluripotency. In Zebrafish, this remodeling is achieved by the maternal methylome becoming hypomethylated to match the paternal methylome. However, how this is achieved in medaka (another teleost fish) is currently not known. Moreover, how DNA methylation remodeling is impacted in hybrid organisms, and the effects this may have on their development, is also not known. Here we address these questions by generation whole genome bisulfite sequencing data for zebrafish, medaka and zebrafish medaka embryos.
Project description:HuR shRNA adenoviruses were delivered into WT or humanized mice intravenously at 2 × 109 pfu/mouse for both control virus and HuR shRNA virus . After seven days, liver tissue samples were harvested after a four hours fasting and stored immediately in liquid nitrogen till further analysis.The frozen liver tissue samples were homogenized in Trizol reagent (Invitrogen) using TissueLyser LT system (Qiagen). The isolated RNA was purified by MagMAX RNA Extraction Kit (ThermoFisher) and the construction of strand specific sequencing libraries using TruSeq Stranded Total RNA Prep kit (Illumina) and the sequencing was performed at NHLBI DNA Sequencing and Genomics Core using Illumina HiSeq 3000 paired-end sequencing platform.
Project description:The involvement of miRNAs during vertebrate oogenesis is poorly documented. Based on the assumption that ovarian-specific or ovarian-predominant genes usually play important roles during oogenesis, we searched for ovarian-predominant miRNAs in the medaka (Oryzias latipes) ovary. 10 tissus were collected from adult medaka (intestine, ovary, testis, liver, heart, gills, kidney, brain, muscle and bone) and RNAs were hybridized on a designed agilent microarray displaying 3800 distinct miRNAs from different teleost and vertebrate species. We identified 66 miRNAs sequences predominantly expressed in the ovary that had never been previously described in medaka.
Project description:Total RNA was extracted from WT or KO liver tumor tissues. RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 2500 platform was used to sequence the RNA samples for the subsequent generation of raw data. KEGG pathway and GSEA enrichment analysis were used for functional pathway analysis.
