GEO DataSets

(Submitter supplied) Mouse somatic cells can be chemically reprogrammed into pluripotent stem cells (CiPSCs) through an intermediate extraembryonic endoderm (XEN)-like state. However, it is elusive how the chemicals orchestrate the cell fate alteration. In this study, we analyze molecular dynamics in chemical reprogramming from fibroblasts to a XEN-like state. We find that Sox17 is initially activated by the chemical cocktails, and XEN cell fate specialization is subsequently mediated by Sox17 activated expression of other XEN master genes, such as Sall4 and Gata4. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

10 Samples

Download data: CSV, XLSX

(Submitter supplied) Somatic cells can be chemically reprogrammed into a pluripotent stem cell (CiPSC) state, mediated by an extraembryonic endoderm- (XEN-) like state. We found that the chemical cocktail applied in CiPSC generation initially activated a plastic state in mouse fibroblasts before transitioning into XEN-like cells. The plastic state was characterized by broadly activated expression of development-associated transcription factors (TFs), such as Sox17, Ascl1, Tbx3, and Nkx6-1, with a more accessible chromatin state indicating an enhanced capability of cell fate conversion. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

35 Samples

Download data: BED, BW, TXT

(Submitter supplied) We report here an approach to redirect somatic cell fate under chemically defined conditions without transcription factors. We start by converting mouse embryonic fibroblasts (MEFs) to epithelial-like cells (ciELC) with chemicals and growth factors. Subsequent cell fate mapping reveals a robust induction of SOX17 in the resulting ELCs that can be further reprogrammed to endodermal progenitor cells (ciEPC). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16417

28 Samples

Download data: CSV, 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) Small-molecule based lineage reprogramming has newly emerged as a promising approach for generating functional cell types. We recently found that the chemical induction of iPSCs from fibroblasts pass through an extra-embryonic endoderm (XEN)-like state. In this study, we demonstrated that these chemically-induced XEN-like cells were not restricted to be reprogrammed to iPSCs, but feasible to be induced into functional neurons, bypassing the pluripotent stage. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

34 Samples

Download data: XLS

(Submitter supplied) RNA-seq data from whole mouse embryos at E3.75 (stage where the three cell types: TE, PrE and EPI are well resolved) and from dissected ICMs in order to identify genes expressed specifically in the ICM

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9318

2 Samples

Download data: TXT

(Submitter supplied) We show here by using genome-wide ChIP-sequencing that lineage segregation involves multiple Sox/Oct partnership. In undifferentiated ES cells Oct4 interacts with Sox2 and both TFs bind on the 'canonical' motif, whereas in cells commited to PrE lineage Oct4 switches from Sox2 to Sox17 interaction and this complex bind to a unique "compressed" motif.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

20 Samples

Download data: TXT, WIG

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6885 GPL6103

15 Samples

Download data

(Submitter supplied) Analysis of the expression of KH2 embryonic stem cells inducibly expressing V5 tagged Sox17 protein. Results provide information on the endodermal gene expression program activated after Sox17 expression in ES cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

10 Samples

Download data: TXT

(Submitter supplied) Analysis of the expression of F9 cells after knockdown of Sox7 and Sox17 during their primitive endoderm differnetiation induction with retinoic acid. Results provide information on the endodermal gene expression program regulated by Sox7 and Sox17.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6103

5 Samples

Download data: TXT

(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) 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

Platforms:

GPL21273 GPL24247

19 Samples

Download data: BW, CSV

(Submitter supplied) Fibroblasts can be chemically induced to pluripotent stem cells (CiPSCs) through an extraembryonic endoderm (XEN)-like state or directly converted into other differentiated cell lineages. However, the mechanisms underlying chemically-induced cell fate reprogramming remain unclear. Here, a transcriptome-based screen of biologically active compounds uncovered that CDK8 inhibition was essential to enable chemically-induced reprogramming from fibroblasts into XEN-like cells, then CiPSCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Fibroblasts can be chemically induced to pluripotent stem cells (CiPSCs) through an extraembryonic endoderm (XEN)-like state or directly converted into other differentiated cell lineages. However, the mechanisms underlying chemically-induced cell fate reprogramming remain unclear. Here, a transcriptome-based screen of biologically active compounds uncovered that CDK8 inhibition was essential to enable chemically-induced reprogramming from fibroblasts into XEN-like cells, then CiPSCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

3 Samples

Download data: CSV

(Submitter supplied) Fibroblasts can be chemically induced to pluripotent stem cells (CiPSCs) through an extraembryonic endoderm (XEN)-like state or directly converted into other differentiated cell lineages. However, the mechanisms underlying chemically-induced cell fate reprogramming remain unclear. Here, a transcriptome-based screen of biologically active compounds uncovered that CDK8 inhibition was essential to enable chemically-induced reprogramming from fibroblasts into XEN-like cells, then CiPSCs. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: BW

(Submitter supplied) Pluripotent stem cells can be generated by pure small molecule compounds. However, only fibroblasts, a heterogeneous cell population, were reported for use in chemical reprogramming, and the efficiency is relatively low, raising the possibility that chemically induced pluripotent stem cells (CiPSCs) are derived from a specific cell subpopulation residing in fibroblast culture. Thus, it is of interest to know whether chemical reprogramming can be induced in other cell types, even using the same chemical cocktail. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) The direct conversion, or trans-differentiation, of non-cardiac cells into cardiomyocytes by forced expression of transcription factors and microRNAs provide promising ways of cardiac regeneration. However, genetic manipulations are still not desirable in real clinical applications. we report the generation of automatically beating cardiomyocyte-like cells from mouse fibroblasts with only chemical cocktails. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

9 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