GEO DataSets

Analysis of blastocyst-derived extra-embryonic endoderm (XEN) cell lines and an embryonic stem (ES) cell line. Results identify independent XEN cell lines that express markers of extra-embryonic endoderm, but not those of the epiblast, and thus represent a new model of an early mammalian lineage.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 cell line, 2 cell type, 3 growth protocol, 3 strain sets

Platform:

GPL81

Series:

GSE2204

4 Samples

Download data: CEL, EXP, RPT

(Submitter supplied) Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1763

Platform:

GPL81

4 Samples

Download data: CEL, EXP, RPT

(Submitter supplied) Comparative analysis of Endodermal-like cell lines with demonstrated ability to support myocardial differentiation

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

9 Samples

Download data: TXT

(Submitter supplied) This analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (K4) TS cells and in female TS cells showing local reversals of imprinted X-chromosome inactivation (K4GFP). Data also includes H3K27me3 ChIP-chip profiles in Eed-/- mutant male and female TS cells obtained from Magnuson laboratory (Kalantry S. et al., Nat Cell Biol, 2006).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14676

10 Samples

Download data: PAIR

(Submitter supplied) We report for the first time, the derivation and characterization of extra-embryonic endoderm (XEN) cells from primitive endoderm (PrE) of porcine (p) embryos. The pXEN cells can be reliably and reproducibly generated from parthenogenic, in vitro or in vivo derived embryos, and express canonical PrE or XEN cell genes (GATA4, GATA6, SOX17, SALL4, FOXA2, and HNF4A). Transcriptome analysis of pXEN cells revealed close resemblance to yolk sac than any other embryonic or extraembryonic tissue. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26285

12 Samples

Download data: XLSX

(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) Expression profiling of mouse embryos at E2.5, E3.5, E4.25, E4.5, E5.5 E6.0 to identify genes regulated during development of the ICM (inner cell mass), TE (Trophectoderm) and PrE (Primative endoderm) Keywords: development

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL519

5 Samples

Download data: GPR

(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) XEN cells are derived from the primitive endoderm of mouse blastocysts. In culture and in chimeras they exhibit properties of parietal endoderm. However, BMP signaling promotes XEN cells to form an epithelium and differentiate into visceral endoderm (VE). Of the several different subtypes of VE described, BMP induces a subtype that is most similar to the VE adjacent to the trophoblast-derived extraembryonic ectoderm. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) We reprot transcriptome states in mouse blastocyst cultured with various conditons as well as Xist deletion. By comparing the gene expression states of blastocyst grown in different culture conditions with Xist deletion, we identified the differentially expressed genes, which are dependent culture conditions and Xist RNA.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

18 Samples

Download data: XLSX

(Submitter supplied) The early mammalian conceptus (blastocyst) contains two supporting extraembryonic tissues - the trophectoderm and the primitive endoderm (PrE) - that encase and guide the epiblast (Epi) to eventually form the all body. Modifications of the conceptus exposed key genes regulating these tissues co-development. However, the combination of signalling pathways at play remains elusive. Stem cell-based models including embryoid bodies and blastoids can be generated in large numbers and subjected to high-content screens. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1955 Samples

Download data: TSV

(Submitter supplied) Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5).

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6246 GPL11533

4 Samples

Download data: CEL, CHP

(Submitter supplied) Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin mono-allelic expression of a small subset of mammalian genes. Imprinted genes have been categorized into two groups: multi lineage (ML) imprinted genes that can show imprinted expression in both embryonic and extra-embryonic lineages, and genes that show extra-embryonic lineage (EXEL) specific imprinted expression restricted to tissues like the placenta and visceral yolk sac (VYS) endoderm. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

19 Samples

Download data: BED, BW, TXT

(Submitter supplied) ATAC-seq, RNA-seq and ChIP-seq in induced TSC and PSC 72 hours past Doxycyclin induction

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

63 Samples

Download data: BED, BIGBED, BIGWIG, TXT

(Submitter supplied) This analysis includes H3K27me3 and H3K4me2 profiles along the length of the X-chromosome in male (F2) and female (F3) TS cells and in male (GHP7/7) and female (GHP7/9) XEN cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14676

14 Samples

Download data: PAIR

(Submitter supplied) Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BED, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

45 Samples

Download data: CSV

(Submitter supplied) To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: CSV

(Submitter supplied) To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

29 Samples

Download data: CSV

(Submitter supplied) It is basically understood that male and female development is initiated by gonad differentiation into either testis or ovary. However, male embryos are reported to develop faster than female during preimplantation, implying sex differences at this stage. To learn more about when sex differentiation begins, we compared the global gene expression pattern of male and female embryos at the blastocyst stage. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL8326 GPL8329

12 Samples

Download data: TXT