GEO DataSets

(Submitter supplied) Long-range chromosomal interaction is an important mechanism by which differentiating cells organise three dimensional promoter-enhancer networks to regulate lineage-specifying, developmental, regulatory genes1,2. Distal promoter contacts in pluripotent stem and specialised cell types, such as foetal liver cells, form co-regulated gene networks correlated with their biological functions1. Promoter interactomes of 17 primary blood cell types also reflect high cell-type specificity3. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15433

3 Samples

Download data: TXT

(Submitter supplied) Profiling global gene expression of undifferentiated human embryonic stem cells, artificially derived cardiomyocytes, fetal ventricular cardiomyocytes, and adult ventricular cardiomyocytes to determine transcriptomic variation between these cell types.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5603

Platform:

GPL6884

10 Samples

Download data: TXT

Analysis of ventricular cardiomyocytes derived from HES2 embryonic stem cells (hESC-VCMs). The in vivo counterparts (undifferentiated HES2 cells, fetal VCMs, and adult VCMs) were also examined. Results provide insight into molecular mechanisms underlying the developmental status of hESC-VCMs.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 cell type sets

Platform:

GPL6884

Series:

GSE50704

10 Samples

Download data

(Submitter supplied) The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells. How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated. Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development. more...

Organism:

Homo sapiens; Callithrix jacchus; Pan paniscus; Pan troglodytes

Type:

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

5 related Platforms

115 Samples

Download data: BW, HIC, RPKM, 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; Expression profiling by array

Platforms:

GPL10999 GPL19171

10 Samples

Download data: BED, CEL, TXT

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL19171

6 Samples

Download data: CEL

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

3 Samples

Download data: BED

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

1 Sample

Download data: TXT

(Submitter supplied) Here, we targeted mCherry to the COUP-TFII genomic locus in NKX2.5eGFP/+ hPSCs. Upon differentiation to atrial and ventricular cardiomyocytes (CMs) this dual atrial COUP-TFIImCherry/+-NKX2.5eGFP/+ reporter line allowed identification and selection of GFP+ (G+)/mCherry+ (M+) CMs following cardiac differentiation. These cells exhibited transcriptional and functional properties of atrial CMs, whereas G+/M- CMs displayed ventricular characteristics. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) We ablated RBM24 from human embryonic stem cells (hESCs) using CRISPR/Cas9 techniques. Although RBM24-/- hESCs still differentiated into sarcomere-hosting cardiomyocytes, they exhibited disrupted sarcomeric structures with punctate Z-lines due to impaired myosin replacement during early myofibrillogenesis. Transcriptomics revealed >4000 genes regulated by RBM24. Among them, core myofibrillogenesis proteins (e.g. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

6 Samples

Download data: TXT, XLSX

(Submitter supplied) RNA sequencing of human embryonic stem cell-derived cardiomyocytes

Organism:

Rattus norvegicus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27452 GPL24676

16 Samples

Download data: CSV, TXT

(Submitter supplied) Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

24 Samples

Download data: BED, TXT

(Submitter supplied) Despite recent progress in mammalian 3D genome studies, it remains experimentally and computationally challenging to identify chromatin interactions genome-wide. Here we developed a highly efficient “easy Hi-C” (eHi-C) protocol that generates high-yield libraries with 0.1 million cells. After rigorous bias-correction with a significantly improved Hi-C analysis pipeline, we can directly recognize the dynamic long- and short-range chromatin loops from contact heatmaps. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Third-party reanalysis; Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL16791 GPL20301

40 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) Despite the growing interest in studying the mammalian genome organization, it is still challenging to map the DNA contacts genome-wide. Here we present easy Hi-C (eHi-C), a highly efficient method for unbiased mapping of 3D genome architecture. The eHi-C protocol only involves a series of enzymatic reactions and maximizes the recovery of DNA products from proximity ligation. We show that eHi-C can be performed with 0.1 million cells and yields high quality libraries comparable to Hi-C.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL11154

10 Samples

Download data: TXT

(Submitter supplied) Lineage commitment is characterised by orchestrated changes in gene expression and chromatin state. Long-range elements such as enhancers coordinate lineage-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. However, the target genes of most long-range elements remain unknown, hindering an integrated understanding of cis-regulatory gene control. Here, we generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

10 Samples

Download data: TXT

(Submitter supplied) ChIP Seq with NKX2-5 antibody in hESC's

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15433

5 Samples

Download data: BED

(Submitter supplied) Differentiation of human pluripotent stem cells (hPSCs) can be used to model human heart development and, in turn, to analyze the developmental consequences of genetic abnormalities. Here, we deleted NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs) and identified a novel genetic interaction between NKX2-5 and HEY2 that is required for heart development

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

6 Samples

Download data: TXT

(Submitter supplied) Myocardial infarction is a major cause of morbidity and mortality worldwide. The limited ability of the surviving cardiac cells to proliferate following an ischemic attack renders the damaged heart susceptible to unfavorable remodeling processes and heart failure. Currently, pharmaceutical and implantable device management of heart failure seek only to preserve existing viable myocardium after an ischemic attack, and thus merely slows the progression of cardiac dysfunction. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3513

Platform:

GPL4133

16 Samples

Download data: TXT

Analysis of cardiomyocytes (CMs) derived from embryonic stem cells (ESCs). Under the appropriate conditions, ex vivo ESCs can differentiate into beating cardiomyocytes via an embryoid body (EB) intermediate. Results provide insight into the mechanisms underlying the differentiation of ESC into CMs.

Organism:

Homo sapiens

Type:

Expression profiling by array, log10 ratio, 4 cell type sets

Platform:

GPL4133

Series:

GSE13834

16 Samples

Download data: TXT

(Submitter supplied) Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression. It is a mystery how chromatin marks in regulatory elements are modulated to establish cell type-specific gene expression. Here we profiled a variety of epigenetic marks in the regulatory elements using massive ChIP-seq (n=84). We uncovered two classes of regulatory elements: Class I was identified with ubiquitous enhancer (H3K4me1) and promoter (H3K4me3) marks in all cell types, whereas Class II was enriched with H3K4me1 and H3K4me3 in a cell type-specific manner. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

96 Samples

Download data: TXT