GEO DataSets

(Submitter supplied) Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) The purpose of this study was to identify Tfap2a binding genome-wide in zebrafish embryos at 24hpf. Tfap2 transcription factors are essential regulators of neural crest development, melanocyte differentiation, and melanoma progression. We aimed to identify Tfap2a-occupied genes to determine direct Tfap2a-regulated transcriptional networks.

Organism:

Danio rerio

Type:

Other

Platform:

GPL24995

2 Samples

Download data: BED, BIGWIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL24247

10 Samples

Download data: MTX, TSV

(Submitter supplied) Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: NARROWPEAK

(Submitter supplied) The Notch pathway is a cell-cell communication system which is critical for many developmental processes, including craniofacial development. Notch receptor activation induces expression of several well-known canonical targets including those encoded by the hes and her genes in mammals and zebrafish, respectively. The function of these genes, individually and in combination, during craniofacial development is not well understood. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

1 Sample

Download data: CSV, RDS

(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) Zebrafish with loss-of-function alx1 mutations develop with craniofacial and ocular defects of variable penetrance, likely due to compensatory upregulation in expression of a paralogous gene, alx3. We show that zebrafish alx1; alx3 mutants develop with highly penetrant cranial and ocular defects that resemble human ALX1-linked FND. alx1 and alx3 are expressed in anterior cranial neural crest (aCNC), which gives rise to the anterior neurocranium (ANC), anterior segment structures of the eye and vascular pericytes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL25922

24 Samples

Download data: RESULTS, TXT

(Submitter supplied) During craniofacial development, different populations of cartilage and bone forming cells develop in precise locations in the head. Most of these cells are derived from pluripotent cranial neural crest cells. The mechanisms that divide neural crest cells into distinct populations are not fully understood. Here we use single-cell RNA sequencing to transcriptomically define different populations of cranial neural crest cells. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

1 Sample

Download data: CSV

(Submitter supplied) Cell fate commitment is a stepwise process, in which multipotent progenitors transition through sequential regulatory states as they become fate restricted. Recent studies have highlighted the extensive transcriptomic shifts that typify cell differentiation, but our understanding of the epigenetic mechanisms underlying these changes is still superficial. To examine how chromatin states are reorganized during cell fate commitment in an in vivo system, we examined the function of pioneer factor Tfap2a at discrete stages of neural crest development. more...

Organism:

Gallus gallus

Type:

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

Platform:

GPL19787

31 Samples

Download data: BW

(Submitter supplied) RNA-seq of RNA isolated from E10.5 mandibular prominence of 3 control and 3 Tfap2a;Tfap2b;Wnt1CRE mutant mouse embryos.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(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) The specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 gains selective access to cartilage-specific cis-regulatory regions during skeletal development had remained unclear. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25922

16 Samples

Download data: NARROWPEAK

(Submitter supplied) RNA-seq transcriptome analysis identified an early requirement for zic2 in periocular neural crest as an activator of alx1, a transcription factor with essential roles in craniofacial and ocular morphogenesis in human and zebrafish

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

9 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL24995

13 Samples

Download data

(Submitter supplied) We have performed single-cell RNA-seq of cranial NC cells in zebrafish over several stages during their migration

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

7 Samples

Download data: CSV