GEO DataSets

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

14 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL13534 GPL11154

50 Samples

Download data: IDAT, WIG

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: WIG

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: XLSX

(Submitter supplied) A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs). At an intermediate reprogramming stage, somatic and pluripotency enhancers are targeted for partial methylation and demethylation. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: TXT

(Submitter supplied) We examined the locations of Cbx3 by chromatin immunoprecipitation in ESCs and pre-iPSCs

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: WIG

(Submitter supplied) Transition from a partially reprogrammed pre-iPSC state to iPSC state can be achieved by modulating levels of histone modifying enzymes or proteins that can bind to histone modifications We used microarrays to determine the gene expression profile of pre-iPSCs depleted for either 3 histone methyltransferases together or the HP1gamma protein

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

878 Samples

Download data: BAM, BED, WIG

(Submitter supplied) Here we performed genome-wide RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS-seq) in isogenic human induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer-derived embryonic stem cells (nt-ESCs), genetically matched in vitro fertilization-derived ESCs (IVF-ESCs), and their respective differentiated cells (cardiomyocytes and endothelial cells). We generated the transcriptome and DNA methylome map in human pluripotent stem cells and their differentiated cells with single-nucleotide resolution. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL17301 GPL16791

54 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array; Methylation profiling by high throughput sequencing

Platforms:

GPL13112 GPL6246

15 Samples

Download data: BED, CEL

(Submitter supplied) We performed 5hmC/5mC DNA Immunoprecipitation followed high-throughput sequencing using the cell sample along the whole TSKM secondary reprogramming system. The TSKM 0D is the fibroblasts deried from TSKM-iPS mouse as the starting cells of the reprogramming.The intermediate cells is 3-days induced cells which are refered as TSKM 3D cells, and the final reprogrammed cells is the iPS cells with full pluripotency driven from this secondary system. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BED

(Submitter supplied) We found that Tet1 (T) can substitute Oct4 and initiates somatic cell reprogramming in combination with Sox2 (S), Klf4 (K) and c-Myc (M). Moreover, the TSKM secondary reprogramming can proceed rapidly with widespread accompanying increase of 5hmC and 5mC at TSS and ES-active regulation regions followed by 5mC-5hmC pattern switchand, and the activation of endogenous Oct4 and Nanog was Tet1 and 5hmC involved in this process. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

9 Samples

Download data: CEL

(Submitter supplied) Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. Human ES cells contain 5-hydroxymethylcytosine (5hmC), which is generated though the oxidation of 5-methylcytosine (5mC) by the TET family of enzymes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

19 Samples

Download data: BED

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL6246 GPL13112

34 Samples

Download data: BED, CEL

(Submitter supplied) Pluripotency can be induced in somatic cells by ectopic expression of defined transcription factors, however the identity of epigenetic regulators driving the progression of cellular reprogramming requires further investigation. Here we uncover a non-redundant role for the JmjC-domain-containing protein histone H3 methylated Lys 27 (H3K27) demethylase Utx, as a critical regulator for the induction, but not for the maintenance, of primed and naïve pluripotency in mice and in humans. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

27 Samples

Download data: BED

(Submitter supplied) Pluripotency can be induced in somatic cells by ectopic expression of defined transcription factors, however the identity of epigenetic regulators driving the progression of cellular reprogramming requires further investigation. Here we uncover a non-redundant role for the JmjC-domain-containing protein histone H3 methylated Lys 27 (H3K27) demethylase Utx, as a critical regulator for the induction, but not for the maintenance, of primed and naïve pluripotency in mice and in humans. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

7 Samples

Download data: CEL

(Submitter supplied) We determined whether the changed imprinted genes are maintained or reverted to the parthenogenetic state when the reprogrammed cells are re-differentiated into specialized cell types. To address this question, we re-differentiated miPSCs into neural stem cells (miPS-NSCs) and compared them with biparental female NSCs (fNSCs) and parthenogenetic NSCs (pNSCs) large-scale gene expression analysis of miPS-NSCs, fNSCs, and pNSCs, using the Illumina gene expression array

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: TXT

(Submitter supplied) Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: H5, TAR

(Submitter supplied) Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL26167 GPL24106

6 Samples

Download data: TAR

(Submitter supplied) Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: BIGWIG