GEO DataSets

(Submitter supplied) Comparison of gene expresion profile of 4 SC clones and 4 SI clones at different time points defined a stabilization competency signiture required for successful reprogramming

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

47 Samples

Download data: TXT

(Submitter supplied) We report the application of enyzme-based 4C-Seq technique for exploring Pou5f1 enhancer interactome in mouse ES cells.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

2 Samples

Download data: BED

(Submitter supplied) We report that Oct4 is modified by O-GlcNAc in stem cells. To find O-GlcNAc-Oct4 target genes, we ChIPed Oct4 with Flag(Oct4) antibody and then O-GlcNAc modified proteins are enriched by sWGA beads (succinylated wheat germ agglutinin (sWGA), which specifically binds O-GlcNAc). Results show that several genes implicated in pluripotency regulation are bound by O-GlcNAc-Oct4 in their gene region.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: TXT, WIG

(Submitter supplied) O-linked-N-acetylglucosamine (O-GlcNAc) has emerged as a critical regulator of diverse cellular processes, but its role in embryonic stem cells (ESCs) and pluripotency has not been investigated. Here we show that O-GlcNAcylation directly regulates core components of the pluripotency network. Blocking O-GlcNAcylation disrupts ESC self-renewal and reprogramming of somatic cells to induced pluripotent stem cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: TXT

(Submitter supplied) iPS cells, produced in in presence of exogeneously expressed E-cadherin and abcence of viral Oct4 were compared with conventional produced OSKM-iPS cells and murine embryonic stem cells (mESCs) or MEFs

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13405

12 Samples

Download data: TXT

(Submitter supplied) We present key transcription factors (TFs) and transcriptional regulatory networks (TRNs) delineating how they control cellular processes related to the SSC reprogramming.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: IDAT

(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:

GPL13112

28 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility of generating patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4 (also known as Pou5f1), Sox2, c-Myc, and Klf4. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

11 Samples

Download data: CEL

(Submitter supplied) RNA transcriptome sequencing (RNA-Seq) and RNA reverse transcription-associated trap sequencing (RAT-Seq) were usded to map long noncoding RNA (lncRNAs) in reprogramming of fibroblasts into pluripotency

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Using RNA reverse transcription-associated trap sequencing (RAT-Seq), we profiled the genome-wide binding gene targets for pluripotency-associated long noncoding RNAs (lncRNAs), including Platr10 (Osclr8), Oeblr20, Oplr16, Palr35, Palr34, Peln1, and Peln4. These datasets will help study the mechanisms underlying the role of lncRNAs in the establishment and maintenance of pluripotency.

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Direct lineage reprogramming represents a remarkable conversion of cellular and transcriptome states. However, the intermediates through which individual cells progress are largely undefined. Here we used single cell RNA-seq at multiple time points to dissect direct reprogramming from mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells. By deconstructing heterogeneity at each time point and ordering cells by transcriptome similarity rather than time we reconstructed a continuous reprogramming path. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

405 Samples

Download data: TXT

(Submitter supplied) Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors. To address this gap,we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification (H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL13112

71 Samples

Download data: BED, BROADPEAK

(Submitter supplied) Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors. To address this gap, we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification (H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL19972

18 Samples

Download data: CEL

(Submitter supplied) Since the initial discovery that OCT4, SOX2, KLF4 and c-MYC overexpression sufficed for the induction of pluripotency in somatic cells, methodologies replacing the original factors have enhanced our understanding of the reprogramming process. However, unlike in mouse, OCT4 has not been replaced successfully during reprogramming of human cells. Here we report on a strategy to do so. Through a combination of transcriptome and bioinformatic analysis we have identified factors previously characterized as being lineage specifiers that are able to replace OCT4 and SOX2 in the reprogramming of human fibroblasts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

16 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

73 Samples

Download data: NARROWPEAK

(Submitter supplied) As somatic cells are converted to iPSCs, their chromatin undergoes wide-ranging rearrangements that affect the ratio of euchromatin-to-heterochromatin, DNA methylation patterns and the regulation of enhancers and promoters. The molecular machinery underlying this process remains largely unknown. Here, we show that Dppa2 and Dppa4, two thus far poorly characterized mES-specific factors, play a key role in resetting the epigenome to a pluripotent configuration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

33 Samples

Download data: TXT