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Links from GEO DataSets

Items: 20

1.

Sox7 and Sox17

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array
Platforms:
GPL6103 GPL6885
15 Samples
Download data
Series
Accession:
GSE43234
ID:
200043234
2.

RNA-sequencing technology identifies specific genes expressed in the ICM of mouse embryos

(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
Series
Accession:
GSE44553
ID:
200044553
3.

Genome-wide maps of Sox/Oct partnerships pluripotent and lineage-committed cells

(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
Series
Accession:
GSE43275
ID:
200043275
4.

Gene expression analysis of V5 tagged Sox17 expressing ES cells

(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
Series
Accession:
GSE43233
ID:
200043233
5.

Gene expression analysis of F9 cells double knock-down for Sox7 and Sox17

(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
Series
Accession:
GSE43232
ID:
200043232
6.

HUES cells: control and overexpressing OCT4

(Submitter supplied) HUES24 cell line was nucleofected with POU5f1 cDNA to overexpress OCT4; This leads to the formation of mesendodermal cells Short- and Long-scales intra- and inter-chromosomal interactions are linked to gene transcription, but the molecular event underlying these structures and how it affects cell fate decision during embryonic development are poorly understood. One of the first embryonic cell fate decisions (i.e mesendoderm determination) is driven by the POU factor OCT4, acting in concert with the high mobility group genes SOX-2 and SOX-17. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL5082
4 Samples
Download data: CEL, XLS
Series
Accession:
GSE58125
ID:
200058125
7.

Gene Expression Analysis of Sox17-induced Mouse Embryonic Stem Cells

(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
Series
Accession:
GSE19028
ID:
200019028
8.

Genome-Wide Sox17 Binding Sites in Mouse Extraembryonic Endoderm and Embryonic Stem Cells

(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
Series
Accession:
GSE19026
ID:
200019026
9.

Cancer-associated missense mutations enhance the pluripotency reprogramming activity of OCT4 and SOX17

(Submitter supplied) The functional consequences of cancer-associated missense mutations are unclear for majority of proteins, here we interrogated cancer mutation databases and identified recurrently mutated positions at structural contact interface of DNA-binding domains of SOX and POU family transcription factors. We used conversion of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs) as a functional read out. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
4 Samples
Download data: TSV
Series
Accession:
GSE134930
ID:
200134930
10.

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(Submitter supplied) Embryonic stem cell (ESCs) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF, Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs or NSCs. Here we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
7 Samples
Download data: WIG
Series
Accession:
GSE69859
ID:
200069859
11.

Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

(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
Series
Accession:
GSE38850
ID:
200038850
12.

ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

(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
Series
Accession:
GSE35496
ID:
200035496
13.

Expression data of human eGFP-SOX17+ endoderm cells

(Submitter supplied) Using homologous recombination in human ESC, we inserted an enhanced green fluorescent protein (eGFP) transgene into a locus encoding a postulated marker of human endoderm, SOX17 in H9 human embryonic stem cells. This allowed purification of SOX17+ hESC endodermal progeny by fluorescence activated cell sorting (FACS) to generate microarray gene expression profile.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
9 Samples
Download data: CEL
Series
Accession:
GSE26862
ID:
200026862
14.

Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

(Submitter supplied) SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self-renewal and differentiation. How temporal fluctuations in their expression levels bias lineage commitment is unknown. Here we generated knock-in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
16 Samples
Download data: BED, BW
Series
Accession:
GSE126554
ID:
200126554
15.

Hhex and Cer1 Mediate the Sox17 Pathway for Cardiac Mesoderm Formation in Embryonic Stem Cells

(Submitter supplied) Cardiac muscle differentiation in vivo is guided by sequential growth factor signals, including endoderm-derived diffusible factors, impinging on cardiogenic genes in the developing mesoderm. Previously, by RNA interference in AB2.2 mouse embryonic stem cells (mESCs), we identified the endodermal transcription factor Sox17 as essential for Mesp1 induction in primitive mesoderm and subsequent cardiac muscle differentiation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
27 Samples
Download data: CEL
Series
Accession:
GSE71528
ID:
200071528
16.

Global gene expression from SOX7 and SOX17 over-expressing human embryonic stem cells (CA1 and CA2 lines)

(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
Series
Accession:
GSE10809
ID:
200010809
17.
Full record GDS3300

SOX transcription factor overexpression in embryonic stem cells

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
DataSet
Accession:
GDS3300
ID:
3300
18.

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

(Submitter supplied) We report the ChIP-seq analysis of Sox17 genome-wide binding and its loss-of-function transcriptomic analysis of both Sox17 and Ctnnb1 (beta-catenin) by RNA-seq.
Organism:
Xenopus tropicalis
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21875
54 Samples
Download data: BED, XLSX
Series
Accession:
GSE148726
ID:
200148726
19.

Chemically-induced reprogramming triggered by Sox17 mediated hierarchical activation of master transcription factors

(Submitter supplied) With the treatment of a cocktail of small molecules, somatic cells can be reprogrammed into pluripotent stem cells (CiPSCs) through an intermediate extraembryonic endoderm (XEN)-like state. However, since none of the chemicals is associated to a specific cell fate, it is elusive how the chemicals orchestrate the cell fate alteration and determination in chemical reprogramming. In this study, we analyze the molecular dynamics in chemical reprogramming process from fibroblasts to XEN-like state, in a time-course manner and in single cell resolution. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21273
10 Samples
Download data: CSV, XLSX
Series
Accession:
GSE144097
ID:
200144097
20.

Expression data from livers in wildtype and Sox17+/-mice at 17dpc

(Submitter supplied) The onset of the liver inflamentation in the Sox17+/- embryos. The expression of Cxcl10, Cxcl2, Cxcl1 and stress-induced heat shock protein Hspa1a and Hspa1b were elevated in Sox17+/- livers at 17dpc, as compared with the wildtype livers.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
4 Samples
Download data: CEL
Series
Accession:
GSE33106
ID:
200033106
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