GEO DataSets

(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) 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) 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

(Submitter supplied) A) We profiled gene expression changes during ES cell differentiation B) We profiled gene expression changes when Pou5f1 or Nanog is knockdown upon RNAi Keywords: Array Based

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1824

Platforms:

GPL1261 GPL3440

32 Samples

Download data: CEL, GPR

Analysis of embryonic stem (ES) cells following RNA interference-mediated depletion of Nanog or Oct4. Nanog and Oct4 are required to maintain the pluripotency and self-renewal of ES cells. Differentially expressed genes scanned for the presence of binding sites for Nanog and Oct4.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 3 protocol sets

Platform:

GPL1261

Series:

GSE4189

14 Samples

Download data: CEL

(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) Global gene expression effects of silencing Jmjd1a and Jmjd2c genes We used microarrays to detail the global programme of gene expression after silencing Jmjd1a gene and Jmjd2c gene separately Keywords: dose response

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3037

Platform:

GPL4234

12 Samples

Download data: JPG, XML

Analysis of embryonic stem (ES) cells following depletion of the histone H3 Lys 9 demethylase genes, Jmjd1a and Jmjd2c. Pluripotent ES cells possess the ability to self-renew indefinitely. Results provide insight into the role of Jmjd1a and Jmjd2c in the maintenance of self-renewal in ES cells.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL4234

Series:

GSE8937

12 Samples

Download data: JPG, XML

(Submitter supplied) Comparison of human embryonic stem cell transcriptome with universal RNA pool (10 human cell lines) to reveal hES cell-specific gene expression. Keywords: cell type comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2507

2 Samples

Download data: TXT

(Submitter supplied) Three transcription factors were silenced in human embryonic carcinoma cells, OCT4, NANOG, and SOX2. Downstream effects were analysed by means of microarrays to obtain insights into the regulation of self-renewal in these cells. Keywords: RNAi-chip

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2507

4 Samples

Download data: TXT

(Submitter supplied) Zfp281 is a partner protein of Nanog. To identify potential target genes of Zfp281, we generated Zfp281 null ESCs using gene targeting, and compared transcriptomic changes between multiple lines of wildtype, heterozygous and null ESCs.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL, TXT

(Submitter supplied) To identify the gene changes after PRDM14 knockdown

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

6 Samples

Download data: TXT

(Submitter supplied) In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs, hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

14 Samples

Download data: TXT

(Submitter supplied) PRDM14 belongs to the PR (PRDI-BF1 and RIZ) domain proteins (PRDM) family which is a subclass of the SET domain proteins, a common domain found in histone modifying enzymes. PRDM14 has been previously implicated to regulate self-renewal of hESCs as knock-down of PRDM14 induced expression of differentiation marker genes and altered the cellular morphology. We showed that PRDM14 directly regulates the expression of key pluripotency gene POU5F1. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: TXT

(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) 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) Targets of putative self-renewal factors Trim28 and Cnot3 in mouse embryonic stem cells were identified by bioChIP-chip (biotin-mediated ChIP-chip). Keywords: Biotin-mediated Chip-chip, Mouse embryonic stem cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

2 Samples

Download data: BAR, BED, CEL

(Submitter supplied) ChIP-seq based determination of CTCF binding sites in embryonic stem cells (ESC)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED

(Submitter supplied) Embryonic stem cells (ESCs) cells run a self-renewal gene expression program, requiring the expression of certain transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs remains enigmatic. Here we show that Cohesin exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL1261 GPL9250

14 Samples

Download data: BED, CEL

(Submitter supplied) ChIP-seq based determination of Rad21 binding sites in embryonic stem cells (ESC) and ESC derived Embryoid Bodies (EB) identified

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED