GEO DataSets

(Submitter supplied) Landmark events occur in a coordinated manner during preimplantation development of the mammalian embryo, yet the regulatory network that orchestrates these events remains largely unknown. We delineated the regulons of Oct4, Sall4, and Nanog using morpholino (MO)-mediated gene knockdowns followed by microarray analysis of pooled embryos.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

42 Samples

Download data: CEL

(Submitter supplied) Embryonic stem cells have potential utility in regenerative medicine due to their pluripotent characteristics. Sall4, a zinc-finger transcription factor, is expressed very early in embryonic development with Oct4 and Nanog, two well characterized pluripotency regulators. Sall4 plays an important role in governing the fate of stem cells through transcriptional regulation of both Oct4 and Nanog. Using chromatin immunoprecipitation coupled to microarray hybridization (ChIP on Chip), we have mapped global gene targets of Sall4 unveiling possible regulation of broad ES cell functions. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6797

2 Samples

Download data: TXT

(Submitter supplied) Gene regulation at the maternal-embryonic transition in the pre-implantation mouse embryo is not well understood. We knock down Ccna2 to establish proof-of-concept that antisense morpholino oligonucleotides can be used to target specific genes. We applied this strategy to study Oct4 and discovered that Oct4 is required prior to blastocyst development. Specifically, gene expression is altered as early as the 2-cell stage in Oct4-knockdown embryos. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) To analyze the role of DNA methylation during differentiation, we performed genome-wide expression analysis of undifferentiated wild type, dnmt1-/- and triple knock out (TKO; dnmt1-/-, dnmt3a-/-, dnmt3b-/-) ESCs as well as respective embryoid bodies (EBs) at two stages of differentiation

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

18 Samples

Download data: CEL

(Submitter supplied) LONG SUMMARY: In this study, we aimed to characterize the function of Tip110 in embryonic development and in mESC survival and self-renewal using a Tip110+/- mouse model. Mating these mice produces wild-type, Tip110+/-, and Tip110-/- offspring. Tip110-/- offspring die early in mouse postimplantation development and mESCs cannot be derived from Tip110-/- blastocysts. Array analysis was performed to gain a better understanding of the underlying molecular mechanisms at play and to appreciate the biological role of Tip110 in embryo and ESC development. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20266

4 Samples

Download data: CEL, CHP

(Submitter supplied) To study the function of Paf1C in mouse ESCs, we generated an ES cell line stably expressing a location and affinity purification (LAP)-tagged Ctr9 fusiuon protein using the bacterial astificial chromosome (BAC)-based TransgeneOmics approach. To investigate whether pluripotency and lineage control genes differentially regulated upon Paf1C depletion are direct targets of the Paf1C, we analyzed the binding of the Ctr9-LAP fusion protein by ChIP-chip and identified 2175 promoter regions that were bound by Ctr9. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5811

1 Sample

Download data: BED, CEL

(Submitter supplied) To monitor global transcript changes after Paf1C depletion we transfected ESCs with esiRNA targeting Ctr9 and control esiRNA (Luc).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) Transcriptome analysis of Oct4 null and wild type preimplantation mouse embryos by RNA-sequencing

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14602

18 Samples

Download data: TXT

(Submitter supplied) BRD4 is an important epigenetic reader implicated in the pathogenesis of a number of different cancers and other diseases. Brd4-null mouse embryos die shortly after implantation and are compromised in their ability to maintain the inner cell mass (ICM), which gives rise to embryonic stem cells (ESCs). We investigated the functions of Brd4 in the ESCs in the present study. To determine the Brd4 target genes in embryonic stem cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL, TXT

(Submitter supplied) In mammalian preimplantation development, pluripotent cells are set aside from cells that contribute to extra-embryonic tissues. Although the pluripotent cell population of mouse and human embryos can be cultured as embryonic stem cells, little is known about the pathways involved in formation of a bovine pluripotent cell population, nor how to maintain these cells in vitro. The objective of this study was to determine the transcriptomic profile related to bovine pluripotency. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL19376

4 Samples

Download data: TXT

(Submitter supplied) Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos but the signalling mechanisms that induce reprogramming are unknown. Here we show that inhibition of Erk1/2 and Gsk3b signalling in mouse embryonic stem cells (ESCs) by small molecule inhibitors (PD0325901 and CHIR99021, hereafter called 2i) induces genome-wide demethylation on a scale similar to that in PGCs and early embryos, with only major satellites, intracisternal A particles (IAPs) and imprinted genes relatively resistant to erasure. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL11002 GPL15103

12 Samples

Download data: TXT

(Submitter supplied) Bright null mouse embryonic stem cells and spontaneously reprogrammed Bright null cells compared to WT mouse embryonic stem cells;Work further described in Popowski et. al 2013 Bright null mouse embryonic stem cells and wildtype mouse embryonic stem cells differentiated in embryoid bodies at day 6 and day 15

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15887

12 Samples

Download data: PAIR

(Submitter supplied) We present a microarray experiment with the same tet-inducible system but with multiple time points within 24 hr to capture early responses to Oct4 suppression. These data were analyzed together with published genome-wide ChIP data. We found that most tentative target genes (TTG) of Oct4 in ES cells were activated by Oct4 and only a few genes were suppressed. The same method was then applied to find target genes of Sox2 and Nanog based mostly on previously published data. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL4358 GPL2549 GPL2552

40 Samples

Download data: TXT

(Submitter supplied) We examined the ability of human NANOGNB to regulate gene expression by ectopically expressing the gene in human dermal fibroblasts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Unlimited self-renewal and developmental pluripotency are hallmarks of embryonic stem cells. Both properties are precisely controlled by the extrinsic signals and intrinsic factors and have been extensively investigated. However, factors capable of converting ES cells to extra-embryonic lineages have been poorly studied. Here we found that overexpression of Ssbp3 dramatically up-regulated trophoblast specific markers. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) A) We profiled gene expression changes during ES cell differentiation B) We profiled gene expression changes when Pou5f1 or Nanog is knockdown upon RNAi Keywords: Array Based

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1824

Platforms:

GPL1261 GPL3440

32 Samples

Download data: CEL, GPR

Analysis of embryonic stem (ES) cells following RNA interference-mediated depletion of Nanog or Oct4. Nanog and Oct4 are required to maintain the pluripotency and self-renewal of ES cells. Differentially expressed genes scanned for the presence of binding sites for Nanog and Oct4.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 3 protocol sets

Platform:

GPL1261

Series:

GSE4189

14 Samples

Download data: CEL

(Submitter supplied) To characterize the differentiation by Sox2 KO, we performed microarray analyses of mouse ES cell line 2TS22C during the time-course being induced of Sox2 KO Keywords: development or differentiation design,time series design

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4358

12 Samples

Download data: TIFF, TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL15520 GPL16417

336 Samples

Download data

(Submitter supplied) Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL16417 GPL15520

244 Samples

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