GEO DataSets

(Submitter supplied) An NFkB target gene array (Panomics, Inc., Redwood City, CA) was performed to profile the expression pattern of 107 NFkB-regulated genes in mouse embryonic stem cells. A small scale microarray was carried out using NFkB target gene array kit (Panomics, Inc., Redwood City, CA). A long sense-strand oligonucleotide for each of the 107 human genes that have been previously shown to be regulated by NFkB signaling pathway was spotted in duplicate on the nitrocellulose membrane. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6239

2 Samples

Download data: TIFF

(Submitter supplied) To investigate the importance of STAT3 in the establishment of ES cells we have in a first step derived stable pluripotent embryonic stem cells from transgenic FVB mice expressing a conditional tamoxifen dependent STAT3-MER fusion protein. In a second step, STAT3-MER overexpressing cells were used to identify STAT3 pathway-related genes by expression profiling in order to identify new key-players involved in maintenance of pluripotency in ES cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS3444 GDS3445 GDS3446

Platforms:

GPL83 GPL81 GPL82

18 Samples

Download data: CEL, CHP

Analysis of cultured embryonic stem (ES) cells overexpressing the transcription factor STAT3. STAT3 is a downstream target of the LIF signaling cascade. LIF activation maintains ES cells in a pluripotent state. Results provide insight into the role of STAT3 in maintenance of ES cell pluripotency.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL83

Series:

GSE11398

6 Samples

Download data: CEL, CHP

Analysis of cultured embryonic stem (ES) cells overexpressing the transcription factor STAT3. STAT3 is a downstream target of the LIF signaling cascade. LIF activation maintains ES cells in a pluripotent state. Results provide insight into the role of STAT3 in maintenance of ES cell pluripotency.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL82

Series:

GSE11398

6 Samples

Download data: CEL, CHP

Analysis of cultured embryonic stem (ES) cells overexpressing the transcription factor STAT3. STAT3 is a downstream target of the LIF signaling cascade. LIF activation maintains ES cells in a pluripotent state. Results provide insight into the role of STAT3 in maintenance of ES cell pluripotency.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL81

Series:

GSE11398

6 Samples

Download data: CEL, CHP

(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) Although much is known about the pluripotency self-renewal circuitry, the molecular events that lead embryonic stem cells (ESCs) exit from pluripotency and begin differentiation are largely unknown. We found that the zinc finger transcription factor Snai1, involved in gastrulation and epithelial- mesenchymal transition (EMT) is already expressed in the inner cell mass of the preimplantation blastocysts. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5807

Platform:

GPL6887

6 Samples

Download data: TXT

Analysis of ESC line E14 expressing 4-hydroxytamoxifen (4-OHT)-inducible Snai1-ER at various time points of induction with 4-OHT. Snai1 (Snail homolog 1) is a member of the Snail family of zinc finger transcription factors. Results provide insight into the role of Snai1 in ESC differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent, 6 time sets

Platform:

GPL6887

Series:

GSE57854

6 Samples

Download data

(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

4 Samples

Download data: BED, TXT

(Submitter supplied) Nanog is a master pluripotency factor of embryonic stem cells (ESCs). Stable expression of Nanog is required to maintain the stemness of ESCs, although Nanog is a short-lived protein and quickly degraded by the ubiquitin-dependent proteasome system (UPS). Here, we report that the deubiquitinase USP21 interacts with, deubiquitinates and stabilizes Nanog and therefore maintains the protein level of Nanog in mouse-ESCs (mESCs). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: BED

(Submitter supplied) Ubiquitination-mediated protein degradation of key transcriptional factors is important to the self-renewal of embryonic stem (ES) cells. However, little is known about the deubiquitination in ES self-renewal and differentiation. Here, we report that deubiquitinase USP21 is an important positive regulator to keep ES cells under undifferentiation stasus by deubiquitination and stabilization of Nanog, a key transcriptional factor of ES cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Embryonic stem (ES) cells continuously decide whether to maintain pluripotency or differentiate. While exogenous LIF and BMP4 perpetuate a pluripotent state, less is known about factors initiating differentiation. We show that heparan sulfate (HS) proteoglycans are critical co-receptors for signals inducing ES cell differentiation. Genetic targeting of NDST1 and 2, two enzymes required for N-sulfation of proteoglycans, blocked differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

16 Samples

Download data: TXT

(Submitter supplied) To characterize the differentiation by Sox2 KO, we performed microarray analyses of mouse ES cell line 2TS22C during the time-course being induced of Sox2 KO Keywords: development or differentiation design,time series design

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4358

12 Samples

Download data: TIFF, TXT

(Submitter supplied) The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED, WIG

(Submitter supplied) The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESCs) and has been implicated in mESC maintenance. Here we demonstrate that, unlike genetic deletion, RNAi-mediated depletion of Tet1 in mESCs led to a significant reduction in 5hmC and loss of mESC identity. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL14661

8 Samples

Download data: CEL

(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:

GPL14661 GPL9250

12 Samples

Download data: BED, CEL, WIG

(Submitter supplied) We generated Nanog-/- iPSCs from both EpiSCs and pre-iPSCs. We wanted to compare the global gene expression profile of these iPSCs to their parental cells lines and to wild-type and Nanog-/- ESCs.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) Mouse embryonic stem cells (mES) were depleted of Klf2, Klf4, and Klf5 by ectopic expression of shRNA. Control RNAi was performed using shRNA against luciferase. At 2 days, 4 days and 6 days post-transfection of shRNA-encoding vectors, cells are harvested for RNA isolation. Keywords: RNAi expression, Mouse ES cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6238

18 Samples

Download data

(Submitter supplied) Performing Chromatin IP of Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells with NimbleGen custom genomic tiling arrays, we sought to decipher Klf2, Klf4, Klf5-regulated genes. Keywords: genomic tiling arrays, ES cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6182

15 Samples

Download data: GFF, PROBE

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

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6238 GPL6182

33 Samples

Download data: GFF, PROBE