GEO DataSets

(Submitter supplied) Waardenburg Syndrome (WS) is a rare genetic disorder that leads to congenital hearing loss and pigmentation defects. MITF is one of its pathogenic genes. While studied extensively in animal models, its pathogenic mechanism still poorly described in humans due to the challenges in accessing embryonic tissues. In recent years, patient-derived human induced pluripotent stem cells(iPSCs) technology offers a promising approach for modeling human melanocyte development and hereditary disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT

(Submitter supplied) The melan-a cell line is derived from immortalized mouse melanocytes obtained from Ink4a-ARF-/- mice. RNA-seq was performed to assess the global nature of transcript and gene expression profiles in melan-a cells. These RNA-seq data, along with separate ChIP-seq performed in melan-a cells (GSE38498), were used to correlate gene expression patterns with the presence or absence of transcription factors of interest.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) Damage to the gene regulatory network governing terminal differentiation of melanocytes leads to pigmentation phenotypes and increases the risk for melanoma. Microphthalmia-associated transcription factor (MITF) directly activates expression of melanocyte differentiation effectors, and levels of MITF have been proposed to govern the melanoma phenotype. Mutations in the gene encoding Transcription Factor Activator Protein 2 alpha (TFAP2A) cause reduced pigmentation in model organisms and premature hair graying in humans, and TFAP2A expression tends to be lower in advanced melanoma tumors than in benign nevi. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9442

2 Samples

Download data: BED

(Submitter supplied) Key to effective gene regulation in development and homeostasis is the ability of transcription factors to discriminate between different classes of binding sites. Yet how this is achieved is poorly understood. The microphthalmia-associated transcription factor MITF is a lineage-survival oncogene that plays a crucial role in melanoma and melanocyte development where it suppresses invasion but promotes both proliferation and differentiation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

21 Samples

Download data: BEDGRAPH

(Submitter supplied) To clarify the effect of Mitf mutation on stria vascularis transcriptome and identify downstream-genes of Mitf pathway which responsible for hearing development, we employed high-throughput sequencing to analyze the transcriptome of MitfR/r and Mitfr/r stria vascularis.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11429

2 Samples

Download data: TXT

(Submitter supplied) Whole genome genotyping (WGG) arrays are the powerful tools for GWAS in farm animal. Here we take advantage of the commercial Illumina PorcineSNP60 BeadChips, a mapping population including 101 individuals were genotyped. Association analysis and linkage analysis were followed to map the causative gene of hearing loss in Chinese Rongchang pigs.

Organism:

Sus scrofa

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL11379

101 Samples

Download data: IDAT

(Submitter supplied) scRNA-seq on GFP + cells sorted from the Tg(mitfa:GFP) transgenic zebrafish embryos at 28 hours post fertilization (hpf) using the 10x Chromium system

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

1 Sample

Download data: MTX, TSV

(Submitter supplied) In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that Tfap2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express Tfap2 paralogs. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

46 Samples

Download data: BW, XLSX

(Submitter supplied) TFAP2A and MITF binding sites were identified in SK-MEL-28 cell lines using Cleavage Under Targets and Release Using Nuclease (CUT&RUN).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: BW

(Submitter supplied) To gain further insights into the specificity of SMCHD1 mutations and identify pathways associated with the disease phenotypes, we have derived induced pluripotent stem cells from patients affected with BAMS or FSHD. We then differentiated these cells into neural crest stem cells, corresponding to the cell type that is mainly affected in BAMS and analyzed their transcriptome by RNA Seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TSV