GEO DataSets

(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) 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) 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) The first lineage decisions during mouse development lead to establishment of embryonic and extraembryonic tissues. The transcription factor Cdx2 plays a central role by repressing pluripotency genes, such as Oct4 and promoting trophoblast fate at the blastocyst stage. Here we show that the transcription factor Gata3 is coexpressed with Cdx2 in the blastocyst and that overexpression of Gata3 in embryonic stem cells is sufficient to induce expression of trophoblast genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS3948 GDS3949

Platform:

GPL1261

24 Samples

Download data: CEL, CHP

(Submitter supplied) To identify whether Cdx2 or Gata3 can activate trophoblast specific gene expression when expressed in R1 ES cells. To assess the dependency of Gata3 activity on Cdx2, Gata3 was also expressed in Cdx2-null ES cells. Keywords: gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL, CHP

(Submitter supplied) To characterized the changes in gene expression during the differentiation of TS cells. TS cells can be derived from two time point during embryogenesis, cell lines tested were from each of these time points. Keywords: time course

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

14 Samples

Download data: CEL, CHP

Analysis of R1 embryonic stem (ES) cells overexpressing transcription factor Cdx2 or Gata3 and cultured under trophoblast stem (TS) cell derivation conditions. Gata3-expressing Cdx2-null ES cells also examined. Results provide insight into the roles of Gata3 and Cdx2 in trophoblast development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 3 protocol sets

Platform:

GPL1261

Series:

GSE12999

10 Samples

Download data: CEL, CHP

Analysis of trophoblast stem (TS) cell lines TS3.5 and TS6.5 derived from 2 time points during embryogenesis (from blastocyst and E6.5 embryos, respectively) and differentiated over 6 days. Results provide insight into the molecular basis of trophoblast development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 cell line, 2 protocol, 7 time sets

Platform:

GPL1261

Series:

GSE12999

14 Samples

Download data: CEL, CHP

(Submitter supplied) In order to study early developmental events in the mammalian embryo it is often desirable to be able to impair expression of specific genes. While DNA and RNA methods are routine, protein methods are still at the very beginning. When a specific antibody is supplied to mouse oocytes expressing the ubiquitin-protein ligase TRIM21, a ternary complex forms with the target protein, leading to its rapid and acute degradation - hence the name 'Trim-away' (PMID 29153837). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20775

6 Samples

Download data: CEL

(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) We report the whole transcriptome data of single-cells derived from the early 16-cell stage to the 64-cell stage in the mouse embryo.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

262 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL8321 GPL17021

19 Samples

Download data: CEL, TXT

(Submitter supplied) Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: TXT

(Submitter supplied) Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

12 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) Current understandings of the initiation of the trophectoderm (TE) program in mammalian embryonic development lacks evidence of how TE-associated factors such as CDX2 and GATA3 participate in bovine lineage specification. In this study, we describe the effects of TE-associated factors on lineage specification marker genes such as SOX2, OCT4, NANOG, GATA6 and SOX17, assisted by a cytosine base editor system. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

11 Samples

Download data: TXT

(Submitter supplied) Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. more...

Organism:

Homo sapiens; Mus musculus; Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112 GPL18648

195 Samples

Download data: TXT

(Submitter supplied) Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to inner cell mass (ICM), where pluripotent epiblast arises, and extraembryonic trophectoderm. While much has been learned about pluripotency regulation, how ZGA is connected to the first lineage segregation in early embryos remains elusive. Here, we investigated the role of nuclear receptor transcription factors (NR TFs), whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21273

113 Samples

Download data: BW, 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:

GPL17021 GPL21103

40 Samples

Download data: WIG