GEO DataSets

(Submitter supplied) Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. more...

Organism:

Danio rerio; Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24995 GPL27992

22 Samples

Download data: MTX, TSV

(Submitter supplied) Expression profile of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under constant photoperiodic conditions were obtained by RNA-seq analysis. Monthly transcriptomes under constant photoperiodic conditions identified 518 circannual genes.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33470

20 Samples

Download data: XLSX

(Submitter supplied) Expression profile of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under outdoor natural conditions were obtained by RNA-seq analysis. Monthly transcriptomes for two years identified 3,341 seasonally-oscillating genes.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33470

50 Samples

Download data: XLSX

(Submitter supplied) Expression profile of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under outdoor natural conditions were obtained by RNA-seq analysis. Daily transcriptomes on the four equinoxes/solstices identified 1,381 daily-oscillating genes.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33470

48 Samples

Download data: XLSX

(Submitter supplied) As a heterogeneous reproductive disorder with unclear etiopathogenesis, polycystic ovary syndrome (PCOS) can be caused by genetic, diet, and environmental factors. Bisphenol A (BPA), a global environmental contaminant, can induce PCOS and NAFLD due to direct exposure; however, whether these phenotypes persist in future unexposed generations is not currently understood. We observed genes abnormally expressed in the ovary of BPA lineage, similar to human PCOS patients. more...

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25587

6 Samples

Download data: TSV

(Submitter supplied) To elucidate molecular mechanisms contributing to the disease phenotype in col10a1 medaka (Oryzias latipes) mutants, we isolated col10a1:nlGFP cells from heterozygous col10a1 medaka mutants and wild-type siblings via fluorescence activated cell sorting (FACS) and performed RNA-seq. Comparison of the transcriptome profiles indicated elevated ER stress, dysregulated cell polarity and reduced ECM production in heterozygous col10a1 mutants.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27992

5 Samples

Download data: TXT

(Submitter supplied) To investigate contribution of different UPR pathways to ER stress-induced abnormal heart phenotype in medaka, we generated constitutive XBP1(S) or ATF6(N) expression medaka lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different genotype medaka hearts.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25587

6 Samples

Download data: XLSX

(Submitter supplied) The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Oryzias latifes (Korea native ricefish) upon treatment of mock, ampicillin and erythromycin

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27992

18 Samples

Download data: XLSX

(Submitter supplied) The assembly of the embryo’s primary axis is a fundamental landmark to establish the vertebrate body plan. Although the morphogenetic movements directing cell convergence towards the midline have been described extensively, little is known on how gastrulating cells interpret mechanical cues. Yap proteins are well-known transcriptional mechanotransducers, yet their role in gastrulation remains elusive. more...

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23308

10 Samples

Download data: BW, TXT

(Submitter supplied) Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. It communicates the needs of the organism to different organs by secreting hormones into the bloodstream. Here, we have used the model fish medaka (Oryzias latipes) to investigate the developmental dynamics in the pituitary using a comprehensive RNA-seq time series from 31 to 375 days post-fertilization.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27992

84 Samples

Download data: XLSX

(Submitter supplied) The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animal’s physiology and development, including growth, reproduction, homeostasis, metabolism and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types are still poorly understood. more...

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23039

2 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) We employed a transgenic strain of a small aquarium fish medaka (Oryzias latipes) that overexpresses a malignant melanoma driver gene. In this model, melanoma develops with 100 % penetrance. Using the medaka malignant melanoma model, we tested whether cisplatin and trametinib are able to suppress the transcriptomic changes induced by the transgene.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17089

60 Samples

Download data: CSV

(Submitter supplied) Transplanted zebrafish blasstomeres into a medaka host develop into a retina that expresses retinal genes

Organism:

Danio rerio; Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28493 GPL20828 GPL23039

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryzias latipes; Mus musculus; Danio rerio

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21493 GPL18413 GPL23444

48 Samples

Download data

(Submitter supplied) DNA methylation is a universal epigenetic mechanism involved in regulation of gene expression and genome stability. The DNA maintenance methylase DNMT1 ensures that DNA methylation patterns are faithfully transmitted to daughter cells during cell division. Because DNMT1 is essential for cell viability, little is known about its tissue-specific function. To overcome this impediment, forward genetic screens were conducted in medaka and zebrafish to identify viable dnmt1 alleles. more...

Organism:

Oryzias latipes

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23444

6 Samples

Download data: TSV

(Submitter supplied) medaka testies transcriptome were sequenced using RNA-seq

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23308

27 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Chromatin accessibility of nine embryonic samples was profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.

Organism:

Oryzias latipes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25587

18 Samples

Download data: BED, BW

(Submitter supplied) We collected ten embryonic stages covering cleavage, blastula, gastrula, somite, and late stages until hatching. We also collected two adult tissue samples, including ovary and testis. 13 samples were sequenced using the illumina short-read sequencing platform.

Organism:

Oryzias latipes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17089 GPL25587

24 Samples

Download data: FA, GFF3, TAB, TXT

(Submitter supplied) Japanese medaka (Oryzias latipes) embryos were exposed to two concentrations of the water accommodated fractions and chemically-enhanced water accommodated fractions of two types of diluted bitumen (dilbit). Chemical-dispersion did not significantly alter transcriptional responses to dilbit toxicity but may have acted through alternative mechanisms to give similar phenotypic responses, such as normal swim bladder development. more...

Organism:

Oryzias latipes

Type:

Expression profiling by array

Platform:

GPL27958

31 Samples

Download data: TXT

(Submitter supplied) We compared the gene expression of whole brain between DMSO- and celastrol-treated medaka.

Organism:

Oryzias latipes

Type:

Expression profiling by array

Platform:

GPL23001

8 Samples

Download data: TXT