Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Oryzias melastigma

PROVIDER: GSE42696 | GEO | 2014/07/01

SECONDARY ACCESSION(S): PRJNA182747

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomic characterization of transcription activator-like effector nucleases-induced XY dmy- sex reversal female medaka (Oryzias latipes)

Project description:We assembled transcription activator-like effector nucleases (TALENs) targeting the DMY gene and generated XYdmy- mutants to investigate gonadal dysgenesis in medaka. RNA-seq generated 157 million raw reads from WT male (WT_M_TE), WT female (WT_F_OV) and XYdmy- female medaka (TA_F_OV) gonad libraries. Differential expression analysis identified 144 up- and 293 downregulated genes in TA_F_OV compared to WT_F_OV, 387 up- and 338 downregulated genes in TA_F_OV compared to WT_M_TE.

2017-02-11 | GSE62700 | GEO

Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos

Project description:Transcriptomic profile of Stage 40 Oryzias latipes (Medaka) embryos wild type and KO for SEDL

2024-05-03 | GSE143538 | GEO

Transcriptome profile of Stage 40 Oryzias latipes (Medaka) embryos II

Project description:In order to identify the effects of the absence of SEDL on Medaka transcriptome, we performed RNAseq experiments Transcriptome analysis of the liver of mice trated with CD95 activating antibody, compared with liver of mice trated with saline.

2024-05-03 | GSE186769 | GEO

Identification of novel ovarian predominant miRNAs in medaka

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.

2016-08-31 | GSE80823 | GEO

Marine medaka (Oryzias melastigma) gill

Project description:Marine medaka gill microbiota

| PRJNA702883 | ENA

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

Molecular analysis of population and De Novo transcriptome sequencing of Thai medaka, Oryzias minutillus (Teleostei: Adrianichthyidae)

Project description:We report the transcriptome sequencing of Thai medaka

2019-07-08 | GSE133888 | GEO

sRNA sequencing of mature and developing gonads during protandrous changes in the Asian seabass

Project description:Purpose: sRNA-sequencing of mature and intermediate gonadal tissue in order to identify the differential expression of miRNAs during male to female (i.e. protandrous) sex transition Methods: Total RNA was extracted and sRNA was purified. cDNA libraries were constructed using a high definition adapter protocol (Xu et al. 2015). 50 bp sequencing was performed on Illumina's HiSeq 2500 at the Earlham Institute, Norwich, UK. Sequenced data was trimmed for adapters and filtered to remove very short and low complexity sequences. miRBase animal miRNA precursor sequences were mapped against the Asian seabass genome in order to generate a set of putative miRNA precursors. Putative precursor molecules with aligning mature miRBase miRNA(s) and forming a valid pre-miRNA hairpin structure were annotated as valid precursor miRNAs. Novel precursor and mature miRNAs were annotated using a combination of published algorithms and manual checking to ensure consistency with canonical miRNA biogenesis criteria. The alignment of sequenced reads against a non-redundant miRNA precursor set was used to determine raw read counts of mature miRNAs. Differential expression analysis was performed in order to identify differentially expressed mature miRNAs between conditions. Results: We detect 156, 71, 122, 151, 171 and 155 differentially expressed miRNA for the testis -> T1/T2, T1/T2 -> T3/T4, T3/T4 -> ovary, testis -> T3/T4, T1/T2 -> ovary and the testis->ovary comparisons respectively Conclusions: There is substantial differential expression of miRNAs at every stage of gonadal change in the Asian seabass during the sex transition process

2022-10-20 | GSE122720 | GEO

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

Gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) in wild type and olvl28m13 knockout Medaka fish (Oryzias latipes)

Project description:To examine the transcriptome, we compared the gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) between wild type medaka and olvl28m13 knockout medaka.

2019-04-08 | GSE119838 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data