GEO DataSets

(Submitter supplied) We report a novel culture condition inducing naive pluripotency in hESCs in a rapid, robust and reproducible way. These naive hESCs were similar to mESCs exhibiting domed colony morphology, increased single survival, reduced doubling time, upregulation of naive pluripotency-specific genes, unbiased lineage-specific differentiation, hypomethylation, separate clustering profile from parental primed hESCs and were dependent on signalling pathways similar to naive mESCs.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

6 Samples

Download data: TXT

(Submitter supplied) Currently, there is only minimal information elucidating the transcriptional changes occurring during the in vitro transition of the inner cell mass (ICM) towards the human embryonic stem cell (hESC) stage and the role played by the post inner cell mass intermediate (PICMI). In this study, we perform in-depth analysis of the transcriptional heterogeneity between these three stages of hESC derivation in order to correlate their downstream effects on pluripotency states and differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: CSV

(Submitter supplied) Human embryonic stem cells (hESCs) hold great value for future clinical applications. However, standard culture conditions maintain hESCs in a primed state, which bears heterogeneity and a tendency for spontaneous differentiation. To counter these drawbacks, hESCs have been converted to a naive state, but this has in turn restricted the efficiency of existing directed differentiation protocols. We show that adaptation of hESCs to Wnt-inhibiting condition (Wnt-i) conferred a unique transcriptional signature with high levels of pluripotency markers and reduced levels of differentiation markers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

72 Samples

Download data: CSV

(Submitter supplied) Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs’ regulation of pluripotency and naïve pluripotency derivation. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL20301

28 Samples

Download data: BED, CSV

(Submitter supplied) Telomere length heterogeneity in various cell types including stem cells and cancer cells has been recognized. Cell heterogeneity also is found in pluripotent stem cells such as embryonic stem cells (ESCs). The implication and mechanisms underlying the heterogeneity remain to be defined. We have optimized a robust method that can simultaneously measure telomere length coupled with RNA-sequencing analysis (scT&R-seq) in the same human ES cell. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

121 Samples

Download data: TXT

(Submitter supplied) Human embryonic stem cells (hESCs) typically exhibit "primed" pluripotency, analogous to stem cells derived from the mouse post-implantation epiblast. This has led to a search for growth conditions that support self-renewal of hESCs akin to hypomethylated naïve epiblast cells in human pre-implantation embryos. We have discovered that reverting primed hESCs to a hypomethylated naïve state or deriving a new hESC line under naïve conditions results in the establishment of Stage Specific Embryonic Antigen 4 (SSEA4) negative hESC lines with a transcriptional program resembling the human pre-implantation epiblast. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

43 Samples

Download data: TAB, TXT

(Submitter supplied) To study the occupancy by EP300 throughout the genome.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) In order to study the occupancy by OGA throughout the genome.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLS

(Submitter supplied) In order to study which part, if any, of the EP300 phenotype is related to OGA regulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: XLS

(Submitter supplied) In order to study the effect of OGA knockdown on naive hESC and its transition to the primed state, we knocked down OGA in PXGL-naive hESC and transformed it into the primed state，as well as collected RNA samples during and after transformation to performe RNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: XLSX

(Submitter supplied) The balance between glycolytic and oxidative metabolism shifts during differentiation of human embryonic stem cells (hESCs) and during reprogramming of somatic cells into pluripotent stem cells. However the contribution of glycolytic metabolism to various stages of pluripotency is not well understood. Additionally, few tools have been developed that modulate pluripotent stem cell glycolytic metabolism to influence self-renewal or differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 Samples

Download data: CEL

(Submitter supplied) Global DNA CpG methylation profiling of human embryonic stem cells, fibroblast iPSC, and low passage stromal primed myeloid iPSC before and after conversion to the naïve state

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

24 Samples

Download data: TXT

(Submitter supplied) Global gene expression analysis of human embryonic stem cells, fibroblast iPSC, and low passage stromal primed myeloid iPSC before and after conversion to the naïve state

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

24 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

4 related Platforms

207 Samples

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(Submitter supplied) Global gene expression analysis of (a) human embryonic stem cells, (b) low passage episomal stromal-primed iPSC derived from growth-factor activated CD34+ myeloid progenitors from cord blood or GCSF mobilized peripheral blood, and (d) samples of donor fibroblasts or myeloid progenitors

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

29 Samples

Download data: TXT

(Submitter supplied) Global gene expression analysis of (a) human embryonic stem cells, (b) adult fibroblasts with and without nucleofection of SOKM, (c) CD34+ cord blood cells at various time points during induction of pluripotency with SOKM, with or without co-culture with bone marrow stromal cells (BMSC), and (d) resulting stromal primed and non-stromal primed cord blood CD34+ myeloid iPSC

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

46 Samples

Download data: TXT

(Submitter supplied) Global CpG methylation profiling using Illumina 27k Infinium platform of (a) human embryonic stem cells, (b) low passage episomal stromal-primed myeloid iPSC, (c) intermediate passage fibroblast iPSC, and (d) samples of corresponding donor cells.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

43 Samples

Download data: TXT

(Submitter supplied) Global gene expression analysis of (a) human embryonic stem cells, (b) low passage episomal stromal-primed myeloid iPSC, (c) intermediate passage fibroblast iPSC, and (d) samples of corresponding donor cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16700

41 Samples

Download data: TXT

(Submitter supplied) Polycomb repressive complex 2 and the epigenetic mark that it deposits, H3K27me3, are evolutionarily conserved and play critical roles in development and cancer. However, their roles in cell fate decisions in early embryonic development remain poorly understood. Here we report that knockout of polycomb repressive complex 2 genes in human embryonic stem cells causes pluripotency loss and spontaneous differentiation toward a meso-endoderm fate, owing to de-repression of BMP signalling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

19 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

23 Samples

Download data: TXT