GEO DataSets

(Submitter supplied) Starvation is a severe form of malnutrition that occurs when an individual's intake of food is inadequate to meet their body's energy requirements. Prolonged starvation can cause permanent organ damage, stunted growth in children, and death if left untreated. It is estimated that approximately 45% of deaths among children under the age of 5 years are linked to undernutrition. Notably, the liver’s health is compromised during starvation. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

12 Samples

Download data: CSV

(Submitter supplied) Liver-derived cells from the surface and cave-adapted morphs of Astyanax mexicanus are valuable in vitro resources to explore the metabolism of these unique fish. However, 2D cultures have not yet fully mimicked the metabolic profile of the fish liver. Also, 3D culturing can modulate the transcriptomic profile of cells when compared to its 2D counterpart. Hence, to widen the range of metabolic pathways that can be depicted in vitro, we cultured the liver-derived SFL and CFL into 3D spheroids. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

8 Samples

Download data: TXT

(Submitter supplied) We report the shift in skeletal muscle investment strategies of the Mexican cavefish following cave colonization

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

17 Samples

Download data: TXT

(Submitter supplied) Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

1 Sample

Download data: MTX, TSV

(Submitter supplied) To test wheather cavefish have higher lipogenesis capability than surface fish, we used liver sample from fasted and refed fish to do RNA-seq to compare their transcriptome responding to feeding in surface fish and Pachón cavefish. Moreover, we did the Pparγ ChIP-seq with liver from fed surface fish and Pachón cavefish. We amied to test whether Pparγ in Pachón cavefish have more biding sites and higher binding peaks than surface fish.

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30057 GPL27684

18 Samples

Download data: BW, CSV

(Submitter supplied) Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

6 Samples

Download data: TXT

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

Organism:

Astyanax mexicanus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL27684 GPL24492

38 Samples

Download data: BED

(Submitter supplied) Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24492

6 Samples

Download data: TXT

(Submitter supplied) Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. more...

Organism:

Astyanax mexicanus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24492

26 Samples

Download data: BED

(Submitter supplied) Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. more...

Organism:

Astyanax mexicanus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27684

6 Samples

Download data: BED

(Submitter supplied) Reduced parasitic infection rates in the developed world are suspected to underlie the rising prevalence of autoimmune disorders. However, the long-term evolutionary consequences of decreased parasite exposure on an immune system are not well understood. We used the Mexican tetra Astyanax mexicanus to understand how loss of parasite diversity influences the evolutionary trajectory of the vertebrate immune system, by comparing river with cave morphotypes. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24492 GPL27942

10 Samples

Download data: H5

(Submitter supplied) Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. more...

Organism:

Astyanax mexicanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27684

12 Samples

Download data: CSV

(Submitter supplied) Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss of eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus1-6, no inactivating mutations have been found in any of these genes2,3,7-10. more...

Organism:

Astyanax mexicanus

Type:

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

Platform:

GPL24492

6 Samples

Download data: TXT