GEO DataSets

(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; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL11154

35 Samples

Download data: BED, BW, XLSX

(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

(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:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: XLSX

(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) Purpose: Assess changes in p63 binding in human embryonic stem cells and surface ectoderm; evaluate differences in the following histone marks: H3K27me3, H3K27ac, H3K4me1, and H3K4me3 in the surface ectoderm with and without p63; and examine changes in H3K27me3 between human embyronic stem cells and surface ectoderm with and without p63. Methods: p63 ChIP-seq libraries were generated in p63 gain-of-function human embryonic stem cells and wild-type surface ectoderm. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

27 Samples

Download data: BED, BROADPEAK, NARROWPEAK

(Submitter supplied) Purpose: Evaluate p63 regulation of gene expression in human embryonic stem cells and the surface ectoderm Methods: RNA profiles for human embyronic stem cells and surface ectoderm cells with and without p63 using deep sequencing, in duplicate, on Illumina NextSeq 500 sequencer. Quality of reads were checked by fastqc. Reads were aligned to hg19 genome using tophat and FPKM values were generated using Homer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) Purpose: Assess changes in the three-dimensional (3D) chromatin architecture during surface ectoderm commitment and evaluate changes in 3D chromatin architecture in human embryonic stem cells and surface ectoderm cells with and without p63. Methods: Cohesin HiChIP profiles for human embryonic stem cells and surface ectoderm cells with and without p63 were generated in triplicate with deep sequencing on the Illumina HiSeq 4000 sequencer. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: BED, MATRIX, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL20301

61 Samples

Download data: BED, BROADPEAK, NARROWPEAK

(Submitter supplied) Purpose: Evaluate changes in chromatin accessibility between human embryonic stem cells and surface ectoderm cells with and without the transcription factor p63. Method: Chromatin accessibility profiles for human embryonic stem cells and surface ectoderm with and without p63 were generated by deep sequencing, in duplicate, with the Illumina NextSeq sequencer. Quality reads were assessed by fastq. Reads were aligned using Bowtie2, PCR duplicates and mitochondrial DNA were discarded, and peak calling was completed using MACS2. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BED

(Submitter supplied) Purpose: Validate HiChIP-identified long-range chromatin interactions at the TFAP2C locus, in a viewpoint-specific manner. Methods: UMI-4C libraries targeting 3 individual viewpoints at the TFAP2C locus were generated in duplicate, in surface ectoderm cells with and without p63. Replicates were sequenced on Illumina NextSeq sequencer, and reads were aligned and filtered for valid long-range interactions using HiCPro. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BED

(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:

GPL24247

54 Samples

Download data

(Submitter supplied) Embryos originate from fertilized eggs and are shaped through continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was found to be essential in initiating the earliest cell fate decisions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: XLSX

(Submitter supplied) Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass (ICM) and trophectoderm (TE) of blastocysts, prompting inquiry into its function in post-lineage establishment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

42 Samples

Download data: BW

(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) 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) We report here genome wide identification of p63 binding sites in cycling neonatal foreskin keratinocytes using high throughput sequencing of ChIP enriched DNA. Analysis of gene ontology, database mining with integration with publicly available data, reveals a role for p63 in transcriptional regulation of multiple genes genetically linked to cleft palate. In addition, we identify AP-2α, a transcription factor which, when mutated, also results in craniofacial clefting syndrome, as a co-regulator of p63 responsive genes.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: BED, WIG

(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