Similar studies for GEO DataSets (Select 200122936) - GEO DataSets

Select item 2001229361.

BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [RNA-Seq]

(Submitter supplied) Mouse naive and primed pluripotent stem cells, ESC and EpiSC, represent two distinct stages of pluripotency. Here we report that BMP4 drives primed to naive transition or PNT by reprogramming chromatin accessibility. ATAC-seq reveals that a short pulse of BMP4 triggers EpiSCs to close 26409 and open 6428 loci to reach an intermediate state that continue to open 18744 and close 7042 loci under 2iL until reaching a naive state, following with a dramatic reactivation of the silenced X chromosome. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
6 Samples

Download data: TSV

Series

Accession:: GSE122936

ID:: 200122936

PubMed Similar studies SRA Run Selector

Select item 2001466532.

BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [ChIP-Seq]

(Submitter supplied) BMP4 regulates a plethora of developmental processes including dorsal-ventral axis and neural patterning. Here we report that BMP4 reconfigures nuclear archi-tecture during primed to naive transition (PNT). We first established a robust BMP4 driven PNT and shown by ATAC- and RNA-seq that it orchestrates the chromatin accessibility dynamics during PNT. Among the loci opened early by BMP4, we identified Zbtb7a/b as new targets that contribute to drive PNT. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21273
2 Samples

Download data: BED, BW

Series

Accession:: GSE146653

ID:: 200146653

PubMed Similar studies SRA Run Selector

Select item 2001229373.

BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility

(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:: GPL21273 GPL19057
17 Samples

Download data: BED, BW

Series

Accession:: GSE122937

ID:: 200122937

PubMed Similar studies

Select item 2001229354.

BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [ATAC-Seq]

(Submitter supplied) Mouse naive and primed pluripotent stem cells, ESC and EpiSC, represent two distinct stages of pluripotency. Here we report that BMP4 drives primed to naive transition or PNT by reprogramming chromatin accessibility. ATAC-seq reveals that a short pulse of BMP4 triggers EpiSCs to close 26409 and open 6428 loci to reach an intermediate state that continue to open 18744 and close 7042 loci under 2iL until reaching a naive state, following with a dramatic reactivation of the silenced X chromosome. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19057
9 Samples

Download data: BW

Series

Accession:: GSE122935

ID:: 200122935

PubMed Similar studies SRA Run Selector

Select item 2000719335.

NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGC) in mice1, where its precise role is yet unclear2-4. We investigated this in an in vitro model, where naïve pluripotent embryonic stem cells (ESCs) cultured in bFGF/ActivinA develop as epiblast-like cells (EpiLCs), and gain competence for PGC-like fate5. Consequently, bone morphogenetic protein (BMP4), or ectopic expression of key germline transcription factors Prdm1/ Prdm14/ Tfap2c, directly induce PGC-like cells (PGCLCs) in EpiLCs, but not in ESCs6-8. more...

Organism:: Mus musculus

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

Platforms:: GPL6887 GPL13112
18 Samples

Download data: BEDGRAPH

Series

Accession:: GSE71933

ID:: 200071933

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000719326.

NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers [ChIP-seq]

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGCs) in mice, where its precise role is yet unclear. We investigated this in an in vitro model, in which naive pluripotent embryonic stem (ES) cells cultured in basic fibroblast growth factor (bFGF) and activin A develop as epiblast-like cells (EpiLCs) and gain competence for a PGC-like fate. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL13112
12 Samples

Download data: BEDGRAPH

Series

Accession:: GSE71932

ID:: 200071932

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000619247.

NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers [microarray]

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGC) in mice1, where its precise role is yet unclear2-4. We investigated this in an in vitro model, where naïve pluripotent embryonic stem cells (ESCs) cultured in bFGF/ActivinA develop as epiblast-like cells (EpiLCs), and gain competence for PGC-like fate5. Consequently, bone morphogenetic protein (BMP4), or ectopic expression of key germline transcription factors Prdm1/ Prdm14/ Tfap2c, directly induce PGC-like cells (PGCLCs) in EpiLCs, but not in ESCs6-8. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
6 Samples

Download data: TXT

Series

Accession:: GSE61924

ID:: 200061924

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000585208.

Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed pluripotent cells

(Submitter supplied) We utilized FAIRE-seq to identify accesible chromatin in mouse embryonic-, epiblast-, and neural- stem cells in addition to mouse embryonic fibroblasts. Analysis of these data sets reveal cell type specific chromatin signatures that differentiate naïve and primed pluripotency. Functional analysis of type-specific peaks revealed cell-type specific enhancers.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11002
10 Samples

Download data: BED, WIG

Series

Accession:: GSE58520

ID:: 200058520

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Select item 2000455099.

Prdm14

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

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
12 Samples

Download data

Series

Accession:: GSE45509

ID:: 200045509

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004550810.

Genome-wide identification of genes differentially expressed between control and Prdm14 overexpressing ES cells grown in serum conditions.

(Submitter supplied) Analysis of Prdm14 function in mouse embryonic stem cells. Prdm14 null and overexpressing ES cells were generated and analyzed by microarray, immunoflurescence, flow cytometry, ELISA, qPCR in different culture conditions.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
6 Samples

Download data: TXT

Series

Accession:: GSE45508

ID:: 200045508

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004550711.

Genome-wide identification of genes differentially expressed between wild-type and Prdm14-deficient ES cells grown in 2i culture conditions.

(Submitter supplied) Analysis of Prdm14 function in mouse embryonic stem cells. Prdm14 null and overexpressing ES cells were generated and analyzed by microarray, immunoflurescence, flow cytometry, ELISA, qPCR in different culture conditions.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6887
6 Samples

Download data: TXT

Series

Accession:: GSE45507

ID:: 200045507

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Select item 20014572712.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL19057 GPL17021
23 Samples

Download data: TXT

Series

Accession:: GSE145727

ID:: 200145727

PubMed Similar studies

Select item 20014572613.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19057
6 Samples

Download data: TXT

Series

Accession:: GSE145726

ID:: 200145726

PubMed Similar studies SRA Run Selector

Select item 20011223414.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) Upon implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked, and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL19057
4 Samples

Download data: BED, BW

Series

Accession:: GSE112234

ID:: 200112234

PubMed Similar studies SRA Run Selector

Select item 20010576215.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
17 Samples

Download data: TXT, XLSX

Series

Accession:: GSE105762

ID:: 200105762

PubMed Similar studies SRA Run Selector

Select item 20014486916.

Coordination of germ-layer lineage choice by TET1 during primed pluripotency

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

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL17021 GPL21103
28 Samples

Download data

Series

Accession:: GSE144869

ID:: 200144869

PubMed Full text in PMC Similar studies

Select item 20014486817.

Coordination of germ-layer lineage choice by TET1 during primed pluripotency (ChIP-seq)

(Submitter supplied) Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL21103 GPL17021
16 Samples

Download data: BW

Series

Accession:: GSE144868

ID:: 200144868

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014486718.

Coordination of germ-layer lineage choice by TET1 during primed pluripotency (ATAC-seq)

(Submitter supplied) Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21103
12 Samples

Download data: BW

Series

Accession:: GSE144867

ID:: 200144867

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012305519.

Formative transition of human naïve pluripotent stem cells

(Submitter supplied) Human naïve pluripotent stem cells (PSC) share features with pre-implantation epiblast. They thus provide an unmatched opportunity for characterising the developmental programme of pluripotency in Homo sapiens. Here we confirm that naïve PSC do not respond directly to germ layer induction, but must first acquire competence. Capacitation for multi-lineage differentiation occurs without exogenous growth factor stimulation and is facilitated by inhibition of Wnt signalling. more...