GEO DataSets

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Oreochromis niloticus; Maylandia zebra; Astatotilapia calliptera; Tropheops sp. 'mauve'; Pundamilia nyererei; Haplochromis burtoni

Type:

Expression profiling by high throughput sequencing

6 related Platforms

40 Samples

Download data: TXT

(Submitter supplied) East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. more...

Organism:

Tropheops sp. 'mauve'; Astatotilapia calliptera; Pundamilia nyererei; Oreochromis niloticus; Haplochromis burtoni; Maylandia zebra

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

(Submitter supplied) As a precise and efficient genetic engineering method, gene editing technology for animals and plants will gradually move towards large-scale applications, and will have a disruptive impact on the breeding of related traits. By using antisense RNA interference technology to interfere with the mRNA expression and protein translation of the SF-1 gene, we have successfully cultivated tilapia with defective gonadal development. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29385

12 Samples

Download data: XLSX

(Submitter supplied) Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalance and suffer from fatty liver disease during the intensive farming. Long non-coding RNAs (lncRNAs) performed essential roles in varieties of biological processes, including lipid metabolism. However, the lncRNAs regarding hepatic lipid metabolism in tilapia have not been identified. In this study, Illumina sequencing and bioinformatic analysis was performed on the liver of male GIFT juvenile fed with high-fat diet (HFD, 18.5% lipid) or normal-fat diet (NFD, 8% lipid) for 56 days. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL29385

6 Samples

Download data: XLSX

(Submitter supplied) Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

6 Samples

Download data: XLSX

(Submitter supplied) Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. more...

Organism:

Oreochromis niloticus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23067

6 Samples

Download data: XLSX

(Submitter supplied) Introduction: reproduction in fish, as in all vertebrates, is regulated by GnRH control on gonadotropic hormones (GTH) activity. However, the neuroendocrine factors that promote GnRH and GTH activity are unknown. In Nile tilapia (Oreochromis niloticus), sexual activity and the ability to reproduce depend on social rank; only dominant males and females reproduce. Here, this characteristic of dominant fish allows us to compare brain and pituitary gene expression in animals that do and do not reproduce, aiming to reveal mechanisms that regulate reproduction. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23067

12 Samples

Download data: TXT

(Submitter supplied) We report an association of DNA hydroxymethylation profiling at single nucleotide resolution with gene expression in the fast muscle of Nile tilapia.

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

5 Samples

Download data: TXT

(Submitter supplied) Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). more...

Organism:

Oreochromis niloticus; Pundamilia nyererei

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23067 GPL28548

6 Samples

Download data: TXT

(Submitter supplied) Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

6 Samples

Download data: XLSX

(Submitter supplied) From mammals to fish, gametogenesis and sexual maturation are driven by luteinizing hormone (LH) and follicle-stimulating hormone (FSH), the gonadotropic hormones temporally secreted from the pituitary. Teleost fish are an excellent model for addressing the unique regulation and function of each gonadotropin cell because, unlike mammals, they synthesize and secrete LH and FSH from distinct cells. Only two very distant vertebrate classes (fish and birds), demonstrate the mono-hormonal strategy suggesting a potential convergent evolution. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23067

24 Samples

Download data: TXT

(Submitter supplied) Background: The historically recent domestication of fishes has been essential for mankind due to the overexploitation of natural stocks and the increasing protein demand to meet the needs of a growing human population. Selection for relevant traits, such as growth, during domestication is a complex process whose epigenetic basis is poorly understood. Results: We have determined changes that occur in the muscle transcriptome after a single generation of Nile tilapia (Oreochromis niloticus) domestication. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

12 Samples

Download data: CSV

(Submitter supplied) This study examines genomic copy-number variation between two African cichlid species through array comparative genomic hybridization. Probe level hybridization ratios were compared to copy number variation identified in Illumina and Pacific Biosciences genome assemblies from both species. Array comparative genomic hybridization was performed with 3 samples (1 replicate array setup) of genomic DNA from Maylandia zebra vs. more...

Organism:

Haplochromis burtoni; Neolamprologus brichardi; Oreochromis niloticus; Maylandia zebra; Pundamilia nyererei

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25405

4 Samples

Download data: PAIR, TXT

(Submitter supplied) GIFT is a type of freshwater farmed fish with high economic value and nutritional value. The liver is an important organ of fish metabolism. Once it is damaged or the disease occurs, it will lead to metabolic disorders and decreased disease resistance, and may cause other secondary diseases. In the high-density intensive culture of tilapia, the feed nutrition is not balanced, especially the addition of high-fat feed. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26254

9 Samples

Download data: TXT

(Submitter supplied) This study examines genomic copy-number variation among African cichlids spanning multiple tribes and radiations. We map CNVs and hotspots throughout the Oreochromis niloticus reference genome, categorize gene ontology enrichment within CNV regions, and compare results with sequence-based cichlid phylogenies.

Organism:

Cyathopharynx furcifer; Oreochromis alcalicus; Pseudocrenilabrus multicolor victoriae; Cyprichromis leptosoma; Labeotropheus fuelleborni; Oreochromis ndalalani; Astatotilapia flaviijosephi; Xenotilapia spiloptera; Julidochromis ornatus; Rhamphochromis longiceps; Coptodon fusiforme; Coptodon kottae; Sarotherodon lamprechti; Coptodon zillii; Cyphotilapia frontosa; Lepidiolamprologus elongatus; Sarotherodon melanotheron; Oreochromis grahami; Pungu maclareni; Nyassachromis microcephalus; Tropheops sp. 'red cheek'; Haplochromis thereuterion; Coptodon deckerti; Sarotherodon galilaeus; Tropheus moorii; Haplochromis burtoni; Ophthalmotilapia ventralis; Lobochilotes labiatus; Boulengerochromis microlepis; Neolamprologus brichardi; Eretmodus cyanostictus; Hemichromis fasciatus; Stomatepia mariae; Copadichromis virginalis; Diplotaxodon greenwoodi; Pallidochromis tokolosh; Konia eisentrauti; Benthodesmus elongatus; Oreochromis niloticus; Astatotilapia calliptera; Callochromis macrops; Variabilichromis moorii; Astatoreochromis alluaudi; Paralabidochromis sp.; Astatotilapia bloyeti; Oreochromis latilabris; Maylandia zebra; Copadichromis borleyi; Haplochromis chilotes; Pundamilia nyererei; Neochromis omnicaeruleus; Coptodon ejagham; Sarotherodon knauerae; Rubricatochromis bimaculatus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25405

168 Samples

Download data: PAIR, TXT

(Submitter supplied) The elucidation of microRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus). Our results enlarge vertebrate
miRNAs collection and reveal a notable differential expression of miRNAs arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.

Organism:

Oreochromis niloticus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23168

16 Samples

Download data: XLSX

(Submitter supplied) Purpose: The objective of this study was to identifiy if a low dose of BaP would alter gene expression profiles and key pathways in the liver and testis of adult male tilapia Methods: The liver and testis tissue from the BaP-treated or control groups fish were collected and then total RNA was extracted, RNA integrity (RIN) was evaluated (RIN >7) for Illumina RNA-Seq library construction and Sequencing. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25292

14 Samples

Download data: TXT

(Submitter supplied) Changes in gene expression are thought to be required for maintaining tissue's proper function under cold stress, but little is known about the role of each tissue in setting the cold tolerance ability in fish. Oreochromis niloticus and Danio rerio are two tropical fishes; they differ in their abilities of cold tolerance. In this study, both fishes were exposed to graded cold temperatures, ranging from 28°C to 18°C and 10°C, and the transcriptomes of 8 tissues at each tempeature were sequenced and compared. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19475 GPL19474

21 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of small non-coding RNAs (18-25 nucleotides) that result in RNA silencing and post-transcriptional regulation of gene expression by binding to the 3'-untranslated regions of their target mRNAs. Mature miRNAs are widely reported in plants, animals and some viruses, which involved in the innate immune response, inflammatory diseases, cell signal transduction, and metabolism. more...

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23067

12 Samples

Download data: TXT

(Submitter supplied) We used a RNA-seq approach to determine the effect of 3,5-di-iodothyronine (T2) and 3,5,3'-tri-iodothyronine (T3) exogenous treatment on the transcriptome of tilapia (Oreochromis niloticus) liver, cerebellum, and thalamus-pituitary. We identified a total of 169, 154 and 2863 genes that were Thyroid hormone-regulated (FDR < 0.05) in tilapia cerebellum, thalamus-pituitary and liver, respectively. Among those, 130, 96 and 349 genes were uniquely regulated by T3, whereas 22, 40 and 929 were only regulated by T2 in the cerebellum, thalamus-pituitary and liver.

Organism:

Oreochromis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23168

18 Samples

Download data: TXT