GEO DataSets

(Submitter supplied) Stem cells self-renew or differentiate under the governance of a stem cell-specific transcriptional program with each transcription factor orchestrating the activities of a particular set of genes. Here we demonstrate that a single transcription factor is able to regulate distinct core circuitries in two different blastocyst-derived stem cell lines, embryonic stem (ES) and extra-embryonic endoderm (XEN) cells. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL4129 GPL4128 GPL6103

30 Samples

Download data: TXT

(Submitter supplied) The inner cell mass of the mouse pre-implantation blastocyst is comprised of epiblast progenitor and primitive endoderm cells of which cognate embryonic (mESCs) or extra-embryonic (XEN) stem cell lines can be derived. Importantly, each stem cell type retains the defining properties and lineage restriction of their in vivo tissue of origin. Recently, we demonstrated that XEN-like cells arise within mESC cultures. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

8 Samples

Download data: TXT

(Submitter supplied) To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

6 Samples

Download data: TXT

(Submitter supplied) We investigated whether Sox17 directly or indirectly regulates extraembryonic endoderm gene expression by identifying Sox17 DNA-binding sites using chromatin-immunoprecipitation coupled with whole-genome promoter tiling array analysis (ChIP-Chip). We used the Sox17 and FLAG antibody to ask whether Sox17 was binding directly to the regulatory regions of genes in homogeneous extraembryonic endoderm (XEN) cell lines and in Sox17-inducible mouse embryonic stem (ES) cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BAR, CEL

(Submitter supplied) We derived and describe a novel mouse cell type that we name primitive XEN (pXEN) cells, and compare their gene expression profiles with other stem cell types previously derived from rodent blastocysts.

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18694 GPL17021

12 Samples

Download data: TAB

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platforms:

GPL8733 GPL7363

29 Samples

Download data: CEL

(Submitter supplied) Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8733

6 Samples

Download data: CEL

(Submitter supplied) Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung) We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8733

6 Samples

Download data: CEL

(Submitter supplied) hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm derived tissues: pancreas, liver, gut, lung. We used microarrays to detail the changes in mRNA expression during the transition from pluripotent hESCs into definitive endoderm.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7363

9 Samples

Download data: TXT

(Submitter supplied) Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8733

8 Samples

Download data: CEL

(Submitter supplied) This study aimed to understand the transcriptional networks regulating endoderm specification from HESC and therefore explored the phenotype of CA1 and CA2 HESC constitutively over-expressing SOX7 or SOX17. Cell lines were created using an inducible construct whereby clonal populations containing transgene integration are selected by Neomycin resistance without expressing of the gene of interest (NoCre controls). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3300

Platform:

GPL570

8 Samples

Download data: CEL, CHP

Analysis of CA1 and CA2 embryonic stem cell (ESC) lines over-expressing transcription factor SOX7 or SOX17, producing extraembryonic endoderm and definitive endoderm progenitors, respectively. Results provide insight into the roles of SOX7 and SOX17 as regulators of endoderm differentiation in ESCs.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 cell line, 3 protocol sets

Platform:

GPL570

Series:

GSE10809

8 Samples

Download data: CEL, CHP

(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:

GPL19057

54 Samples

Download data: BED, BW, CSV, TXT

(Submitter supplied) In this study, we characterised transcriptomes of mESC in different conditions EPSCM and KOSR subsetting them for their single expression of SOX2 or the double expression of SOX2 and GATA6 in these conditions. 2iLIF (sorted only by DAPI negative cells) were used as control.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: CSV, TXT

(Submitter supplied) In early mammalian development, cleavage stage blastomeres and cells of the inner cell mass (ICM) of the blastocyst co-express embryonic and extra-embryonic transcriptional determinants. Using a double protein-based reporter we identify embryonic stem cells (ESC) that co-express the extra-embryonic factor GATA6 alongside the embryonic factor SOX2 in specific conditions. Based on single cell transcriptomics we find these population resemble unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence and suggesting they represent an ideal model to determine how GATA6 and SOX2 influence each other's DNA binding. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

53 Samples

Download data: BED, BW

(Submitter supplied) A small number of transcription factors, including Oct-3/4 and Sox2, constitute the transcriptional network that maintains pluripotency in embryonic stem (ES) cells. Previous reports suggested that some of these factors form a complex that binds the Oct-Sox element, a composite sequence consisting of closely juxtaposed Oct-3/4-binding and Sox2-binding sites. However, little is known regarding the components of the complex. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

2 Samples

Download data: BAR, CEL

(Submitter supplied) We detected the gene expression differences between porcine extra-embryonic endoderm cells and naïve like and primed porcine ESCs. Gene expression of porcine extra-embryonic endoderm cells was distinct with porcine naïve like and primed embryonic stem cells. Pearson correlation analysis confirmed that porcine naïve like and primed ESCs have stronger correlation than the correlation between either pXEN cells and porcine naïve like ESCs or primed ESCs. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

7 Samples

Download data: TXT

(Submitter supplied) Identification of transcripts in different subpopulations of the HIV mouse ES cell line growing under self-renewing conditions (+Lif, +10FCS, GMEM media and plated on gelatin coated dishes). Subpopulations were identified and isolated based on the expression of the cell surface marker, SSEA 1 (a marker of murine ES cells) and expression of the venus protein, the cDNA of which was knocked into the Hex locus (Hhex). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6867

8 Samples

Download data: TXT

(Submitter supplied) Members of the GATA protein family play important roles in lineage specification and transdifferentiation. Previous reports show that some members of GATA protein family also can induce pluripotency in somatic cells by substituting for the key pluripotency-associated factor Oct4. However, the mechanism that links the lineage specifying cues and activation of pluripotency remains elusive. Here, we report that all GATA family members can substitute for Oct4 to induce pluripotency. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

22 Samples

Download data: BED, TXT, WIG

(Submitter supplied) The differentiation to cardiomyocytes is a prerequisite and an important part of heart development. A good understanding of the complicated cardiomyocyte differentiation process benefits cardiogenesis study. Embryonic stem cells (ESCs), cell lines with infinite ability to proliferate and to be differentiated into all cell types of the adult body, are important research tools for investigation of differentiation and meanwhile good models for developmental research. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

8 Samples

Download data: CEL, TXT