GEO DataSets

(Submitter supplied) This study determines the genome-wide binding profile of a V5-tagged KLF5 transription factor exogenously expressed in mouse embryonic stem cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: BW, TXT

(Submitter supplied) This study examines the transcriptomes of embryonic stem cells following overexpression of Klf5. Additionally, this study examines the transcripomes of single embryos either treated with scramble siRNA or siRNA targeting Klf5.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

20 Samples

Download data: TXT

(Submitter supplied) In the preimplantation mouse embryo TEAD4 is critical to establishing the trophectoderm (TE)-specific transcriptional program and segregating TE from the inner cell mass (ICM). However, TEAD4 is expressed both in the TE and the ICM. Thus, differential function of TEAD4 rather than expression itself regulates specification of the first two cell lineages. We used ChIP-seq to define genome-wide TEAD4 target genes and asked how transcription of TEAD4 target genes is specifically maintained in the TE. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BB, BW

(Submitter supplied) Klf5 has essential functions during early embryogenesis and in the derivation of ES cells from inner-cell mass of blastocyst. Among Kruppel-like factor (Klf) family members, only Klf5 shows peri-implantation lethal phenotype, but the precise mechanisms still remain unknown. To understand and identify molecular mechanisms, we performed microarray analysis by using E3.0 WT and Klf5 KO embryos when first phenotype of Klf5 deficiency appears.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL

(Submitter supplied) This study describes the generation and analysis of the transcriptional profile of bovine inner cell mass (ICM) and trophectoderm (TE), obtained from in vivo developed embryos by using a bovine-embryo specific array (EmbryoGENE) containing 37,238 probes.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

8 Samples

Download data: TXT

(Submitter supplied) During the first lineage segregation, a mammalian totipotent embryo differentiates into inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first mouse lineage specification across 6 stages, spanning the pre-initiation, initiation, commitment, and maintenance phases. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL18480 GPL21273 GPL24247

93 Samples

Download data: BW, TXT

(Submitter supplied) Single cell transcriptome profiling of human naïve embryonic stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: MTX, TSV

(Submitter supplied) Genomic profiling of NANOG binding in KLF4 KLF5 double knockouts naïve human embryonic stem cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL21290

41 Samples

Download data: BW, MTX, TSV, TXT

(Submitter supplied) Transcriptome profiling for KLF4 and/or KLF5 knockout lines in human naïve embryonic stem cells Transcriptome profiling for CRISPRa-LTR7Y or KLF5 overexpression in primed human embryonic stem cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

25 Samples

Download data: TXT

(Submitter supplied) We report the genomic binding profile of KLF5, NANOG and H3K27ac in human naïve ESCs

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21290 GPL24676

10 Samples

Download data: BW

(Submitter supplied) ATAC-seq profiling and comparison for chromatin accessibility in human primed embryonic stem cells (ESCs), primed ESCs overexpressing KLF5, and naïve ESCs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BW

(Submitter supplied) Here we provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. We elucidate conserved transcriptional programs along with those that are human-specific. Importantly, we validate our RNA-sequencing findings at the protein level, which further reveals differences in human and mouse embryo gene expression. For example, we identify several genes exclusively expressed in the human pluripotent epiblast including the transcription factor KLF17. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: TXT

(Submitter supplied) Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

124 Samples

Download data: BED, TDF, TXT

(Submitter supplied) Homozygous disruption of Bteb2/Klf5, a homolog of Drosophila gap gene Krüppel, led to increased expression of various differentiation marker genes, such as Fgf5, Cdx2, and Brachyury in mouse ES cells without compromising their ability to differentiate into all three germ layers. Upon removal of LIF, Klf5-deficient ES cells showed faster differentiation kinetics than wild-type ES cells. In contrast, overexpression of Klf5 in ES cells suppressed the transcription of differentiation marker genes, and maintained pluripotency in the absence of LIF. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3509

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

Analysis of embryonic stem cells (ESCs) lacking the transcription factor Klf5. Klf5 deficiency results in the failure of ESC derivation from cells of the inner cell mass and early embryonic lethality. Results provide insight into the role of Klf5 in blastocyst development and ESC self-renewal.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE9244

4 Samples

Download data: CEL, CHP

(Submitter supplied) First lineage specification in the mammalian blastocyst embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to the embryo proper and extraembryonic tissues. We show histone methylation asymmetry on promoters in the first two developmental lineages, and highlight epigenetic skewing associated with derivation of embryonic stem (ES) cells.

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL8943

16 Samples

Download data: PAIR

(Submitter supplied) The histone H3 lysine 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL9185

3 Samples

Download data: BED, TXT

(Submitter supplied) The histone H3 lysine 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3599

Platform:

GPL6333

6 Samples

Download data: TXT

Analysis of embryonic stem (ES) cells following shRNA knock-down of Eset. Eset is a histone H3 lysine 9 (H3K9) methyltransferase critical for development of the inner cell mass (ICM) from which ES cells are derived. Results provide insight into the role of Eset in ES cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 protocol sets

Platform:

GPL6333

Series:

GSE17439

6 Samples

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