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Items: 1 to 20 of 1001

1.

Distinct features of the regenerating heart uncovered through comparative single-cell profiling

(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:
Oryzias latipes; Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27992 GPL24995
22 Samples
Download data: MTX, TSV
Series
Accession:
GSE262689
ID:
200262689
2.

Genome-wide transcriptome analysis of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under constant photoperiodic conditions

(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
Series
Accession:
GSE234565
ID:
200234565
3.

Genome-wide transcriptome analysis of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) kept under outdoor natural conditions over a period of two years

(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
Series
Accession:
GSE234401
ID:
200234401
4.

Genome-wide transcriptome analysis of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of medaka (Oryzias latipes) at the spring equinox, summer solstice, autumn equinox, and winter solstice [24h RNA-seq]

(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
Series
Accession:
GSE234400
ID:
200234400
5.

Transcriptional analysis reveals the progression of PCOS to ovarian cancer in medaka fish ancestrally exposed to BPA

(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
Series
Accession:
GSE226322
ID:
200226322
6.

Gene expression changes in collagen10a1 (col10a1) medaka mutants

(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
Series
Accession:
GSE233581
ID:
200233581
7.

Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

(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
Series
Accession:
GSE215040
ID:
200215040
8.

Genome-wide gene expression Oryzias latipes under antibiotics (ampicillin and erythromycin)

(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
Series
Accession:
GSE205468
ID:
200205468
9.

A Yap-dependent transcriptional program directs cell migration for embryo axis assembly

(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
Series
Accession:
GSE201791
ID:
200201791
10.

A time series of the pituitary gland transcriptome during development and sexual maturation in the model fish medaka

(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
Series
Accession:
GSE179598
ID:
200179598
11.

Characterization of hormone-producing cell types in the medaka pituitary gland using single-cell RNA-seq

(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
Series
Accession:
GSE162787
ID:
200162787
12.

Modulation of medaka transcriptome by trametinib and cisplatin

(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
Series
Accession:
GSE114190
ID:
200114190
13.

Transcriptome analysis of zebrafish, medaka and zebraka chimeras

(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
Series
Accession:
GSE150009
ID:
200150009
14.

Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Oryzias latipes; Mus musculus
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL21493 GPL18413 GPL23444
48 Samples
Download data
Series
Accession:
GSE98648
ID:
200098648
15.

Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 (Medaka)

(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
Series
Accession:
GSE98646
ID:
200098646
16.

RNA-seq testis

(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
Series
Accession:
GSE129727
ID:
200129727
17.

Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis

(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
Series
Accession:
GSE136027
ID:
200136027
18.

Transcriptome profiling of medaka timecourse embryonic samples and adult tissues samples.

(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
Series
Accession:
GSE136018
ID:
200136018
19.

Transcriptional responses in newly-hatched Oryzias latipes associated with developmental malformations following diluted bitumen exposure

(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
Series
Accession:
GSE142734
ID:
200142734
20.

Gene expression of whole brain between DMSO- and celastrol-treated medaka

(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
Series
Accession:
GSE145971
ID:
200145971
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