GEO DataSets

(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 array; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL1261

8 Samples

Download data: CEL

(Submitter supplied) Multipotent spermatogonial stem cells (mSSCs) derived from SSCs are a potential new source of individualized pluripotent cells in regenerate medicine such as ESCs. We hypothesized that the culture-induced reprogramming of SSCs was mediated by a mechanism different from that of iPS, and was due to up-regulation of specific pluripotency-related genes during cultivation. Through a comparative analysis of expression profile data, we try to find cell reprogramming candidate factors from mouse spermatogonial stem cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Spermatogonial stem cells (SSCs) can spontaneously dedifferentiate into embryonic stem cell (ESC)-like cells, which are designated as multipotent SSCs (mSSCs), without ectopic expression of reprogramming factors. SSCs express key OSKM reprogramming factors at some levels, and do not require ectopic expression of any gene for the acquisition of pluripotency during reprogramming to mSSCs. Therefore, we reasoned that additional factors are required to regulate SSC reprogramming. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: TXT

(Submitter supplied) Spermatogonial stem cells (SSCs) have pluripotent potential. However, frequency of pluripotent cell derivation is low and the mechanism of culture-induced reprogramming remains unknown. Here we report that epigenetic instability of germline stem (GS) cells, cultured SSCs, induces pluripotent cell derivation. GS cells undergo DNA demethylation in H19 differentially methylated region under low-density culture. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

46 Samples

Download data: CEL

(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) A single spermatogonial stem cell can aquire pluripotentiality but that conversion into a pluripotent cell type is accompanied by loss of spermatogenic potential. We used microarrays to compare the expression profiles among the different stem cell types. Keywords: cell type comparison

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

(Submitter supplied) In a pilot experiment to reprogramme MEF into endoderm, we infected MEF with the Yamanaka´s factors (O: Oct4, K: Klf4, S: Sox2, M:Myc), FoxA2 (F) and Gata4 (G). Global gene expression of isolated clones was performed.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

13 Samples

Download data: CEL

(Submitter supplied) The in vitro derivation and propagation of spermatogonial stem cells (SSCs) from pluripotent stem cells (PSCs) is a key goal in reproductive science. We show here that when aggregated with embryonic testicular somatic cells (reconstituted testes), primordial germ cell-like cells (PGCLCs) induced from mouse embryonic stem cells differentiate into spermatogonia-like cells in vitro and are expandable as cells that resemble germline stem cells (GSCs), a primary cell line with SSC activity. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

108 Samples

Download data: TXT

(Submitter supplied) The in vitro derivation and propagation of spermatogonial stem cells (SSCs) from pluripotent stem cells (PSCs) is a key goal in reproductive science. We show here that when aggregated with embryonic testicular somatic cells (reconstituted testes), primordial germ cell-like cells (PGCLCs) induced from mouse embryonic stem cells differentiate into spermatogonia-like cells in vitro and are expandable as cells that resemble germline stem cells (GSCs), a primary cell line with SSC activity. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15907

12 Samples

Download data: TXT

(Submitter supplied) We examined global gene expression patterns of mouse embryonic stem cells overexpressing EGFP, Nanog wild-type, or Nanog L122A mutants in normal, "-LIF" or "+RA" culture conditions by RNA-seq experiments. In “+RA” culture conditions, the expression patterns of the RA-responsive genes were slightly different in WT transfectants and more different in L122A transfectants compared with EGFP transfectants. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT, XLS

(Submitter supplied) Pluripotent stem cells can be obtained from spermatogonial stem cells (SSCs) through spontaneous reprogramming without transgenic introduction, but this process is inefficient and lacks mechanism exploration. Here, we reconstructed the progression trajectory of mouse SSC reprogramming by single-cell RNA sequencing and identified a bona fide pluripotent route as the successful reprogramming branch. Notably, we developed five-chemicals combination which could boost the reprogramming efficiency nearly 1000 times than previous study. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL24247

145 Samples

Download data: COV, CSV, TXT, XLSX

(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) 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) We report that Zic3 and Esrrb synergistically enhance the reprogramming efficiency when transduced with Oct4, Sox2 and Klf4 (OSK) into murine fibroblasts. By ChIP-seq analysis, we reveal that Zic3 recruits Esrrb to its own binding sites, some of which are proximal to glycolysis-related genes, thereby cooperatively upregulating these genes to activate glycolytic metabolism, and that Esrrb binds to genes related to mitochondrial oxidative phosphorylation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: TXT

(Submitter supplied) We report that Zic family (Zic1/2/3) and orphan nuclear receptors family (Esrrb and Nr5a2) transcription factors (TFs) synergistically enhance the reprogramming efficiency when transduced with Oct4, Sox2 and Klf4 (OSK) into murine fibroblasts. To identify the molecular mechanisms underlying this synergy, we analyzed global gene expression at 6 days after introduction of reprogramming factors. As a result, we found that primary targets of these TFs are different when either of TFs was introduced with OSK, but a significant portion of genes including pluripotency makers such as Dppa2 was synergistically upregulated. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

18 Samples

Download data: CEL

(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) We provide the genome-wide map of Esrrb binding in mitotic and asynchronous ES cells together with the Esrrb-induced transcriptomic changes in early G1, late G1 and G2.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

30 Samples

Download data: TXT