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Links from GEO DataSets

Items: 20

1.
Full record GDS5400

DPP4A overexpression effect on fibroblast cell line

Analysis 3T3 fibroblast cells overexpressing the pluripotency factor DPPA4. DPPA4 encodes a DNA binding SAP domain-containing protein. Results provide insight into the role of DPPA4 in oncogenesis.
Organism:
Mus musculus
Type:
Expression profiling by array, count, 4 agent sets
Platform:
GPL6885
Series:
GSE58709
8 Samples
Download data
2.

Total Gene expression analysis of Dppa4-trandformed 3T3s

(Submitter supplied) Total gene expression analysis was performed on 3T3s transfomed by SV40, cMyc, or mDppa4 in relative to vector transduced control 3T3s. Intent was to analyze the role of mDppa4 in oncogenic transformation.
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS5400
Platform:
GPL6885
8 Samples
Download data: TXT
Series
Accession:
GSE58709
ID:
200058709
3.

Dppa4 is dispensable for embryonic stem cell identity and germ cell development, but essential for embryogenesis

(Submitter supplied) Dppa4 (Developmental pluripotency-associated 4) has been identified in several highprofile screens as a gene that is expressed exclusively in pluripotent cells. It encodes a nuclear protein with a SAP-like domain and appears to be associated preferentially with transcriptionally active chromatin. Its exquisite expression pattern and results of RNA interference experiments have led to speculation that Dppa4, as well as its nearby homolog Dppa2, might play essential roles in embryonic stem cell function and/or germ cell development. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
6 Samples
Download data: CEL, CHP
Series
Accession:
GSE15173
ID:
200015173
4.

Genome-wide Dppa4 binding in E14 mESC, 3T3, and P19 cells

(Submitter supplied) DPPA4 is a DNA-associated factor that is highly and selectively expressed in embryonic stem cells. DPPA4 expression is strikingly downregulated upon loss of pluripotency, but is reactivated in a number of cancer cell types. It has recently been identified as an oncogene and shown to promote cell proliferation and anchorage independent growth; Dppa4-transformed cells can form tumors in vivo in mice. DPPA4 has been shown to associate with active chromatin and histone H3, but the global binding dynamics of DPPA4 are unknown. Additionally, only several DPPA4 gene targets are known. To better understand the role of DPPA4 in embryonic stem cell pluripotency and oncogenesis, we performed ChIP-Seq in E14 mouse embryonic stem cells (mESC), 3T3 cells ectopically expressing DPPA4, and P19 embryonic carcinoma cells.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: BED
Series
Accession:
GSE95055
ID:
200095055
5.

Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional program

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
90 Samples
Download data
Series
Accession:
GSE120953
ID:
200120953
6.

Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional program [CRISPR-KO]

(Submitter supplied) The molecular regulation of zygotic genome activation (ZGA) in mammals remains poorly understood. Primed mouse embryonic stem cells contain a rare subset of “2C-like” cells that are epigenetically and transcriptionally similar to the two cell embryo and thus represent an ideal system for studying ZGA transcription regulation. Recently, the transcription factor Dux, expressed exclusively in the minor wave of ZGA, was described to activate many downstream ZGA transcripts. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
7 Samples
Download data: TXT
Series
Accession:
GSE120952
ID:
200120952
7.

Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional program [siRNA]

(Submitter supplied) The molecular regulation of zygotic genome activation (ZGA) in mammals remains poorly understood. Primed mouse embryonic stem cells contain a rare subset of “2C-like” cells that are epigenetically and transcriptionally similar to the two cell embryo and thus represent an ideal system for studying ZGA transcription regulation. Recently, the transcription factor Dux, expressed exclusively in the minor wave of ZGA, was described to activate many downstream ZGA transcripts. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: TXT
Series
Accession:
GSE120951
ID:
200120951
8.

Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional program [RNA-seq]

(Submitter supplied) The molecular regulation of zygotic genome activation (ZGA) in mammals remains poorly understood. Primed mouse embryonic stem cells contain a rare subset of “2C-like” cells that are epigenetically and transcriptionally similar to the two cell embryo and thus represent an ideal system for studying ZGA transcription regulation. Recently, the transcription factor Dux, expressed exclusively in the minor wave of ZGA, was described to activate many downstream ZGA transcripts. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
74 Samples
Download data: TXT
Series
Accession:
GSE120950
ID:
200120950
9.

Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL17021
73 Samples
Download data: NARROWPEAK
Series
Accession:
GSE117173
ID:
200117173
10.

Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency (RNA-seq)

(Submitter supplied) As somatic cells are converted to iPSCs, their chromatin undergoes wide-ranging rearrangements that affect the ratio of euchromatin-to-heterochromatin, DNA methylation patterns and the regulation of enhancers and promoters. The molecular machinery underlying this process remains largely unknown. Here, we show that Dppa2 and Dppa4, two thus far poorly characterized mES-specific factors, play a key role in resetting the epigenome to a pluripotent configuration. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
33 Samples
Download data: TXT
Series
Accession:
GSE117172
ID:
200117172
11.

Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency (ChIP-seq)

(Submitter supplied) As somatic cells are converted to iPSCs, their chromatin undergoes wide-ranging rearrangements that affect the ratio of euchromatin-to-heterochromatin, DNA methylation patterns and the regulation of enhancers and promoters. The molecular machinery underlying this process remains largely unknown. Here, we show that Dppa2 and Dppa4, two thus far poorly characterized mES-specific factors, play a key role in resetting the epigenome to a pluripotent configuration. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
40 Samples
Download data: NARROWPEAK
Series
Accession:
GSE117171
ID:
200117171
12.

A genome wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation

(Submitter supplied) Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. Here, we used a genome wide shRNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3, Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation and promoted proliferation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
8 Samples
Download data: TXT
Series
Accession:
GSE32595
ID:
200032595
13.

Extensive SUMO modification of chromatin factors distinguishes pluripotent from somatic cells

(Submitter supplied) The post-translational modification of proteins by SUMO acts as a key gatekeeper of cell identity. In mouse embryonic fibroblast (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct sets of substrates to preserve the somatic and pluripotent states. Using MS-based proteomics, we show here that the composition of the endogenous SUMOylomes differs dramatically between MEFs and ESCs. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL16570
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE144881
ID:
200144881
14.

Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer associated pluripotency genes

(Submitter supplied) BET-regulated transcriptome and BRD4, BRD2, BRD3 and Pol II ChIP-seq datasets in human ESCs before and after BET inhibition. Transcription factors and chromatin remodeling complexes are key determinants of embryonic stem cell (ESC) identity. In this study, we investigate the role of BRD4, a member of the bromodomain and extra-terminal domain (BET) family of epigenetic reader proteins, in control of ESC identity. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154
14 Samples
Download data: BED, TXT, WIG
Series
Accession:
GSE60171
ID:
200060171
15.

Transforming pluripotency: an exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells

(Submitter supplied) Exon-level transcriptome analysis of embryonal carcinoma (EC) and embryonic stem (ES) cell lines. To circumvent difficulties of isolating pure populations of cancer stem cells for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of five embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumour, to their non-malignant caricature, specifically six human embryonic stem (ES) cell lines. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL5188 GPL5175
28 Samples
Download data: CEL, CHP
Series
Accession:
GSE34855
ID:
200034855
16.

S1P mediates key targets associated with survival, proliferation and pluripotency in human embryonic stem cells

(Submitter supplied) Human embryonic stem cells (hESCs) replicate by the process of self-renewal, whilst maintaining their pluripotency. Understanding the pathways involved in the regulation of this self-renewal process will assist in developing fully-defined conditions for the proliferation of hESCS required for therapeutic applications. We previously demonstrated a role for Sphingosine-1-phosphate (S1P) in the survival and proliferation of hESCs. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS2832
Platform:
GPL570
8 Samples
Download data: CEL
Series
Accession:
GSE7896
ID:
200007896
17.
Full record GDS2832

Sphingosine-1-phosphate effect on embryonic stem cells

Analysis of embryonic stem cells (ESCs) after treatment with sphingosine-1-phosphate (S1P) which plays a role in regulation of fate in many cell types. ESCs grown on mouse embryo fibroblast feeder cells and under feeder-free conditions. Results provide insight into the role of S1P in ESC renewal.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 2 agent, 2 growth protocol sets
Platform:
GPL570
Series:
GSE7896
8 Samples
Download data: CEL
DataSet
Accession:
GDS2832
ID:
2832
18.

Gene regulatory networks mediating canonical Wnt signal directed control of pluripotency and differentiation in embryo stem cells

(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:
GPL9250 GPL6246
26 Samples
Download data: BED, CEL, XLS
Series
Accession:
GSE43597
ID:
200043597
19.

ChIP-seq analysis of β-catenin in mouse embryonic stem cells treated with GSK3 inhibitor CHIR99021 under serum+LIF standard condition.

(Submitter supplied) The objective of this study was to identify the direct target genes of β-catenin acting downstream of canonical Wnt signaling in mouse embryonic stem cells (ESCs).Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. Canonical Wnt signaling is intertwined with the pluripotency network comprising Nanog, Oct4, and Sox2 in mouse ESCs. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
5 Samples
Download data: BED, XLS
Series
Accession:
GSE43565
ID:
200043565
20.

Transcriptional responses to GSK3 inhibitor and MEK inhibitor on 2i-adapted mouse embryonic stem cells

(Submitter supplied) The objective of this study was to investigate the roles of GSK3 inhibitor CHIR99021 and MEK inhibitor PD0325901 on 2i-adapted mouse embryonic stem cells (ESCs) in serum-free conditions.Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
15 Samples
Download data: CEL
Series
Accession:
GSE43421
ID:
200043421
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