GEO DataSets

(Submitter supplied) Here we characterized the transcriptome and epigenome of control keratinocytes during differentiation. Epigenomic analyses showed that the temporal enrichment of p63 motifs in dynamic enhancers underscores the key role of p63 in orchestrating the enhancer landscape during keratinocyte differentiation. The cooperation between p63 and its co-regulating factors, such as RUNX1, is important for the finetuning of gene expression.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL11154

18 Samples

Download data: BED, TAB

(Submitter supplied) Here we integrated multi-omics profiles including transcriptomics, DNA accessibility and capture Hi-C data to explore how p63 shapes local chromatin architecture in skin keratinocytes isolated from EEC syndrome patients. Surprisingly, we observed decreased chromatin accessibility in a number of DNA looping nodes which were co-mediated by p63 and CTCF. Our findings not only identified a new aspect of the bookmark function of p63, but also shed light on the disease mechanism underlined p63 dysfunction. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

21 Samples

Download data: TXT, WIG

(Submitter supplied) Tightly controlled gene expression orchestrated by the transcription factor p63 during epithelial differentiation is important for development of epithelial-related structures such as epidermis, limb and craniofacial regions. How p63 regulates spatial and temporal expression of its target genes during these developmental processes is however not yet clear. By epigenomics profiling in stem cells established from one of these epithelial structures, the epidermis, we provide a global map of p63-bound regulatory elements that are categorized as single enhancers and clustered enhancers during epidermal differentiation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: TXT, WIG

(Submitter supplied) Tightly controlled gene expression orchestrated by the transcription factor p63 during epithelial differentiation is important for development of epithelial-related structures such as epidermis, limb and craniofacial regions. How p63 regulates spatial and temporal expression of its target genes during these developmental processes is however not yet clear. By epigenomics profiling in stem cells established from one of these epithelial structures, the epidermis, we provide a global map of p63-bound regulatory elements that are categorized as single enhancers and clustered enhancers during epidermal differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT, WIG

(Submitter supplied) Transcription factor p63 is a key regulator of stratified epithelia. In humans mutations in p63 are associated with developmental disorders that manifest defects in stratified epithelia including the epidermis. We established an epidermal commitment model using human pluripotent stem cells (PSCs) and characterized differentiation defects of PSCs carrying p63 mutations. Transcriptome analyses revealed distinct phases of epidermal commitment, multipotent simple epithelial, basal stratified epithelial and mature epidermal fates. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BW, TXT

(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

Platform:

GPL17021

14 Samples

Download data

(Submitter supplied) Gene expression analysis of two different mouse keratinocytes using RNA-Seq

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) Mapping p63 regulatory and epigenetic landscape in mouse keratinocytes using ChIP-Seq techniques

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: BED, BIGWIG

(Submitter supplied) In this work, we demonstrate that the p53-induced transcriptome is dependent on pre-establishment of cell type-dependent cis-regulatory networks. The epithelial-specific p53 transcriptome is strongly dependent on p63, which acts as a pioneer factor for epithelial-specific enhancers. These results suggest a broad mechanism for regulating the p53-dependent cellular response to stress through differential regulation of cis-regulatory elements and identify p63 as a direct and critical regulator of enhancer activity in epithelial cell types.

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL19057 GPL18573

98 Samples

Download data: BED, BEDGRAPH, BW, NARROWPEAK, TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

48 Samples

Download data: BED, BIGWIG

(Submitter supplied) We report transcriptional changes following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) We report changes in enrichment at chromatin of p63, KLF4 and H3K27ac following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

30 Samples

Download data: BED, BIGWIG

(Submitter supplied) We report changes in chromatin accessibility following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BED, BIGWIG

(Submitter supplied) Somatic differentiation requires induction of lineage specific genes to fulfill specialized tissue functions yet the genomic control of this process is incompletely understood. Using the epidermis as a model, we show here that the BAF chromatin remodeling complex is essential to maintain a subset of open chromatin regions, which are strikingly enriched for the DNA binding motif of the stratified epithelial lineage-determining transcription factor p63 (p=1X10-1786). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

26 Samples

Download data: BED, BROADPEAK, NARROWPEAK, TXT

(Submitter supplied) We analyzed Brg1 binding genomeiwide in freshly isolated newborn mouse epidermal keratinocytes using ChIP-seq technology

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: BED

(Submitter supplied) Changes in global gene expression in the epidermis of the Brg1(i)ep-/- mice in comparison to the wild type at E16.5 were analyzed using micro-array technology.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

1 Sample

Download data: TXT

(Submitter supplied) Development of epidermis includes a complicated program of keratinocyte differentiation. Here we study a new membrane LIM-domain containing Zn-finger protein ZNF185 which is expressed in upper layers of human skin and is up-regulated during keratinocyte differentiation in vitro. Interestingly, depletion of ZNF185 causes delay of keratinocyte differentiation with decreased levels of FLG, LOR, LCEs expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

8 Samples

Download data: TXT

(Submitter supplied) Recent advances in human pluripotent stem cell (hPSC) technology provide a unique resource for skin tissue replacement, but the detailed understanding of regulatory mechanisms limits standardization and broad clinical application. Here, we interrogate chromatin accessibility and transcriptome dynamics during hPSC-derived epidermal differentiation, and discover two critical transition periods: surface ectoderm initiation and keratinocyte maturation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: BEDGRAPH

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL11154

61 Samples

Download data: BEDGRAPH, BW