GEO DataSets

(Submitter supplied) The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although a lot of previous studies have identified key factors regulating this core network in trans, the contribution of cis-regulatory DNA sequences on the transcription of these key pluripotency factors remains elusive. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

7 Samples

Download data: BED

(Submitter supplied) We report the effect on genome-wide gene expression after deletion of an enhancer region downstream of Sox2 in F1 ES cells. The Sox2 transcription factor must be robustly transcribed in embryonic stem (ES) cells to maintain pluripotency.  Reporter assays reveal novel enhancers, including two enhancers over 100 kb downstream (SRR107 and SRR111) which, through the formation of chromatin loops, localise to the Sox2 promoter in ES cells.  Using CRISPR/Cas9 we deleted a region containing these two enhancers, which we term the Sox2 control region (SCR). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL16417

12 Samples

Download data: BEDGRAPH

(Submitter supplied) ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15722

6 Samples

Download data: CEL

(Submitter supplied) We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL13112

30 Samples

Download data: WIG

(Submitter supplied) Esrrb, Sox2 or Esrrb and Sox2 were knocked down in mouse ES cells using shRNA plasmid pSUPER.puro containing shRNAs from the publications Feng et al., 2009 and Rodda et al., 2005. Knockdown was transfected into mouse ES cells using lipofectamine and then cells were selected for knockdown using puromycin. RNA was harvested after 2 days of knockdown.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

4 Samples

Download data: TXT

(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:

GPL17021

7 Samples

Download data: BED, BEDGRAPH, TSV

(Submitter supplied) Super-enhancers (SEs) are large clusters of transcriptional enhancers that are co-occupied by multiple lineage specific transcription factors driving expression of genes that define cell identity. In embryonic stem cells (ESCs), SEs are highly enriched for Oct4, Sox2, and Nanog in the enhanceosome assembly and express enhancer RNAs (eRNAs). We sought to dissect the molecular control mechanism of SE activity and eRNA transcription for pluripotency and reprogramming. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Super-enhancers (SEs) are large clusters of transcriptional enhancers that are co-occupied by multiple lineage specific transcription factors driving expression of genes that define cell identity. In embryonic stem cells (ESCs), SEs are highly enriched for Oct4, Sox2, and Nanog in the enhanceosome assembly and express enhancer RNAs (eRNAs). We sought to dissect the molecular control mechanism of SE activity and eRNA transcription for pluripotency and reprogramming. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TSV

(Submitter supplied) Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a transcription factor BACH1, who which directly interacts with OCT4/SOX2/NANOG (OSN) and MLL/SET1 methyltransferase complexes and maintains pluripotency in mouse ESCs (mESCs). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL24247

23 Samples

Download data: BED, BROADPEAK, NARROWPEAK, XLSX

(Submitter supplied) Mouse ESCs depleted of the epigenetic modifying enzyme Usp22 fail to differentiate properly. Ectopic expresison of Usp22 results in spontaneous differnetiation. In order to understand the transcriptional program underlying this biological defect, whole genome expression analysis was performed.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4973

Platform:

GPL6246

4 Samples

Download data: CEL

Analysis of E14 embryonic stem cells (ESCs) depleted for ubiquitin specific protease 22 (Usp22). ESCs depleted of the epigenetic modifying enzyme Usp22 fail to differentiate properly. Results provide insight into the role of Usp22 in ESC differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL6246

Series:

GSE42934

4 Samples

Download data: CEL

(Submitter supplied) Mapping ultra-high resolution of Sox2:DNA interaction after trichostatin A (TSA) treatment would provide us with valuable new mechanistic insights into how epigenome regulates transcription factor DNA interactions in the cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: TXT

(Submitter supplied) We have profiled the chromosomal contacts of the Sox2 promoter in wild-type ESCs as well as cell lines with a genetically altered Sox2 locus.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

6 Samples

Download data: BW

(Submitter supplied) We recently identified the DNA repair complex XPC-RAD23B-CETN2 as a stem cell coactivator (SCC) required for OCT4 and SOX2 transcriptional activation. Here we investigate genome-wide the role of SCC in murine ESCs by mapping regions bound by its RAD23B subunit in wild type and Xpc-/- ESCs, and analyzing transcriptional profiles of SCC-depleted ESCs.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

10 Samples

Download data: TXT

(Submitter supplied) We characterized a long-range enhancer cluster driving Klf4 expression in naïve pluripotent stem cells. CRISPR/Cas9 mediated screening and genome editing identified DNA motifs corresponding to key pluripotency TFs on these enhancer regions. We employed ChIP-exo genome-wide sequencing to Esrrb and Stat3 in mESCs and validated their functional engagement on the Klf4 enhancer cluster. Moreover, we performed ATAC-seq on wild type and Oct4/Sox2 composite motif biallelic deletion ESCs on Klf4 enhancer E2 to examine the accessible chromatin structure upon loss of lead TFs Oct4 and Sox2 in a single enhancer region.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: BED, TXT

(Submitter supplied) To understand the mechanism underlying the transcriptional regulation by Sox2, we analyzed genome-wide binding sites of Sox2, Tfap2c, and Cdx2 in trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BW

(Submitter supplied) Sox2 is a pleiotropic transcription factor that regulates self-renewal and differentiation capacity in different types of stem cells, raising the possibility that it regulates similar transcriptional programs controlling common stemness. Embryonic stem (ES) cells and trophoblast stem (TS) cells are two developmentally related types of stem cells, which originate from distinct lineages of peri-implantation embryos. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL13112 GPL6096

50 Samples

Download data: BW, CEL

(Submitter supplied) To understand the mechanism underlying the versatility in transcriptional regulation by Sox2 and Esrrb, we compared genome-wide binding sites of Sox2 and Esrrb in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

11 Samples

Download data: BW

(Submitter supplied) To characterize the transdifferentiation of embryonic stem (ES) cells into trophoblast stem (TS) cells triggered by forced repression of Oct3/4, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Oct3/4.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

21 Samples

Download data: CEL

(Submitter supplied) To compare the transcriptional networks governed by Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Sox2 in each cell type.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

12 Samples

Download data: CEL