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Items: 1 to 20 of 819

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

Seasonal transcriptional landscape of medaka brain

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Oryzias latipes
Type:
Expression profiling by array
Platform:
GPL23001
30 Samples
Download data: TXT
Series
Accession:
GSE124988
ID:
200124988
13.

Seasonal changes of gene expression of whole brain in Medaka fish (Oryzias latipes) LW

(Submitter supplied) To examine the seasonal transcriptional landscape of medaka brain, we compared the gene expression of whole brain under SC (short-day and cool temperature conditions: 10 h light/14 h dark and 10 °C) and LW (long-day and warm temperature conditions: 14 h light/10 h dark and 26 °C) conditions.
Organism:
Oryzias latipes
Type:
Expression profiling by array
Platform:
GPL23001
10 Samples
Download data: TXT
Series
Accession:
GSE124985
ID:
200124985
14.

Seasonal changes of gene expression of whole brain in Medaka fish (Oryzias latipes) SC

(Submitter supplied) To examine the seasonal transcriptional landscape of medaka brain, we compared the gene expression of whole brain under SC (short-day and cool temperature conditions: 10 h light/14 h dark and 10 °C) and LW (long-day and warm temperature conditions: 14 h light/10 h dark and 26 °C) conditions.
Organism:
Oryzias latipes
Type:
Expression profiling by array
Platform:
GPL23001
12 Samples
Download data: TXT
Series
Accession:
GSE124973
ID:
200124973
15.

Gene expression profiling for control and high temperature treated Japanese medaka

(Submitter supplied) the experiment was designed to investigate the temperature effect on gene expression
Organism:
Oryzias latipes
Type:
Expression profiling by array
Platform:
GPL28114
16 Samples
Download data: TXT
Series
Accession:
GSE144740
ID:
200144740
16.

Decode-seq: a practical approach to improve differential gene expression analysis

(Submitter supplied) It is often the case that inadequate numbers of biological replicates are utilized in differential gene expression analysis. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling a large number of replicates simultaneously. This approach significantly improved the performance of differential gene expression analysis. Using this approach in medaka fish (Oryzias latipes), we discovered novel genes with sexually dimorphic expression, and genes necessary for germ cell development. more...
Organism:
Mus musculus; Oryzias latipes; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL25587 GPL26363
12 Samples
Download data: TSV
Series
Accession:
GSE130014
ID:
200130014
17.

The gene expression of the brain/pituitary from oxt/oxtr1 homozygous mutants and WT medaka in both sexes

(Submitter supplied) Differential gene expression in the brain/pituitary of oxt/oxtr1 homozygous mutants in both sexes.
Organism:
Oryzias latipes
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24211
18 Samples
Download data: TXT
Series
Accession:
GSE139158
ID:
200139158
18.

Bisulfite sequencing of medaka PGCs methylomes

(Submitter supplied) Medaka PGCs methylomes were sequenced using whole genome bisulfite sequencing (WGBS)
Organism:
Oryzias latipes
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL23039
15 Samples
Download data: BEDGRAPH
Series
Accession:
GSE130002
ID:
200130002
19.

Silver nanocolloids affects glycosylation in medaka fish to cause embryonic malformation.

(Submitter supplied) We observed silver nanocolloids (SNCs) exposure to medaka embryo induced morphological deformities like shortened body and undeveloped head and eyes, and our gene expression analysis using medaka oligo DNA microarray suggested that glycan/glycosylation genes, such as gns and alg2, might be the targets of SNCs' toxicity. Validation studies of gns and alg2 gene expressions by qPCR showed stage-dependent and altered mRNA expression patterns, and their altered expressions were more severe in earlier stages of embryogenesis. more...
Organism:
Oryzias latipes
Type:
Expression profiling by array
Platform:
GPL24183
6 Samples
Download data: TXT
Series
Accession:
GSE106163
ID:
200106163
20.

Identification and functional analysis of yap1b: a new Yap family member in teleosts that evolved a divergent transcriptional activation domain.

(Submitter supplied) The vertebrate paralogs Yap1 and Taz are well known Hippo pathway effectors playing a key regulatory process in growth, morphogenesis, cell survival and cancer progression. Upon translocation to the nucleus Yap/Taz interact with Tead proteins and regulate transcription through their conserved C-terminal activation domain. Here we describe yap1b a new teleost paralog of the Yap1/Taz family that evolved specifically in Euteleostei -the largest clade within vertebrates- by duplication and subsequent adaptation of yap1. more...
Organism:
Danio rerio; Oryzias latipes
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18413 GPL23308
6 Samples
Download data: BED, BW
Series
Accession:
GSE120531
ID:
200120531
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