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:

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

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

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

Organism:

Maylandia zebra

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31192

3 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Here we use single nuclei RNA sequencing (snRNA-seq) of replacement teeth and adjacent oral lamina in Lake Malawi cichlids, species with lifelong whole-tooth replacement, to make two main discoveries. First, despite hundreds of millions of years of evolution, we demonstrate conservation of cell type gene expression across vertebrate teeth (fish, mouse, human). Second, we used an approach that combines marker gene expression and developmental potential of dental cells to uncover the transcriptional signature of stem-like cells in regenerating teeth. more...

Organism:

Maylandia zebra

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31192

1 Sample

Download data: CSV, MTX, TSV

(Submitter supplied) Here we use single nuclei RNA sequencing (snRNA-seq) of replacement teeth and adjacent oral lamina in Lake Malawi cichlids, species with lifelong whole-tooth replacement, to make two main discoveries. First, despite hundreds of millions of years of evolution, we demonstrate conservation of cell type gene expression across vertebrate teeth (fish, mouse, human). Second, we used an approach that combines marker gene expression and developmental potential of dental cells to uncover the transcriptional signature of stem-like cells in regenerating teeth. more...

Organism:

Maylandia zebra

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31192

2 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.

Organism:

Diplotaxodon limnothrissa; Maylandia zebra; Rhamphochromis longiceps; Astatotilapia calliptera; Pundamilia nyererei; Petrotilapia genalutea; Aulonocara stuartgranti

Type:

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

11 related Platforms

60 Samples

Download data: BW, FA, TXT

(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:

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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25405

4 Samples

Download data: PAIR, TXT

(Submitter supplied) We use the continuously replacing dentition of Lake Malawi cichlid fishes to understand de-novo tooth replacement in adult vertebrates. In this system, each tooth is replaced in a one-for-one fashion every ~50 days. Here, we explore the source of epithelial stem cells for tooth replacement.

Organism:

Labeotropheus fuelleborni; Maylandia zebra

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25813 GPL25814

12 Samples

Download data: CSV

(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:

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; 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; Coptodon zillii; Cyphotilapia frontosa; Lepidiolamprologus elongatus; Sarotherodon melanotheron; Oreochromis grahami; Pungu maclareni; Nyassachromis microcephalus; Tropheops sp. 'red cheek'; Haplochromis thereuterion; Coptodon deckerti; 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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL25405

168 Samples

Download data: PAIR, TXT

(Submitter supplied) Array primarily based on tilapia assembly OreNil 1.0, however additional probes were designed to BROAD cichlid assemblies for other available version 1 genomes (https://www.broadinstitute.org/tilapia/tilapia-genome-project) Probes designed to 100% Consensus-Sequence from tilapia genome assembly based on multiple genome alignment of the 5 Cichlid species genome (MAF from Satsuma), with additional probes designed to sequences from multiple non-tilapia species but missing from tilatia genome. more...

Organism:

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

2 Series

172 Samples

Download data: NCD, NDF, POS