Similar studies for GEO DataSets (Select 200260993) - GEO DataSets

Select item 2002609931.

Single-cell 3D genome structure reveals distinct human pluripotent states (CUT&Tag-seq)

(Submitter supplied) Pluripotent states of embryonic stem cells (ESCs) with distinct transcription profile affect their differentiation capacity and therapeutic potential. By single cell analysis of high-resolution three-dimensional (3D) genome structure, we show that remodeling genome structure is highly associated with pluripotent states of human ESCs (hESCs). Naive pluripotent state is featured with specialized 3D genome structures and clear chromatin compartmentation distinct from primed state. more...

Organism:: Homo sapiens

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

Platform:: GPL18460
19 Samples

Download data: BW

Series

Accession:: GSE260993

ID:: 200260993

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Select item 2002609952.

Single-cell 3D genome structure reveals distinct human pluripotent states

(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

Platform:: GPL18460
29 Samples

Download data: BW

Series

Accession:: GSE260995

ID:: 200260995

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Select item 2002609943.

Single-cell 3D genome structure reveals distinct human pluripotent states (RNA-Seq)

(Submitter supplied) Pluripotent states of embryonic stem cells (ESCs) with distinct transcription profile affect their differentiation capacity and therapeutic potential. By single cell analysis of high-resolution three-dimensional (3D) genome structure, we show that remodeling genome structure is highly associated with pluripotent states of human ESCs (hESCs). Naive pluripotent state is featured with specialized 3D genome structures and clear chromatin compartmentation distinct from primed state. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18460
4 Samples

Download data: TXT

Series

Accession:: GSE260994

ID:: 200260994

PubMed Full text in PMC Similar studies

Select item 2002609914.

Single-cell 3D genome structure reveals distinct human pluripotent states (ATAC-Seq)

(Submitter supplied) Pluripotent states of embryonic stem cells (ESCs) with distinct transcription profile affect their differentiation capacity and therapeutic potential. By single cell analysis of high-resolution three-dimensional (3D) genome structure, we show that remodeling genome structure is highly associated with pluripotent states of human ESCs (hESCs). Naive pluripotent state is featured with specialized 3D genome structures and clear chromatin compartmentation distinct from primed state. more...

Organism:: Homo sapiens

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

Platform:: GPL18460
6 Samples

Download data: BW

Series

Accession:: GSE260991

ID:: 200260991

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Select item 2000585205.

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 2001119296.

Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells

(Submitter supplied) Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs’ regulation of pluripotency and naïve pluripotency derivation. more...

Organism:: Homo sapiens

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

Platforms:: GPL24676 GPL20301
28 Samples

Download data: BED, CSV

Series

Accession:: GSE111929

ID:: 200111929

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Select item 2001680027.

Oct4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human

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

Organism:: Homo sapiens

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

Platforms:: GPL18573 GPL24676
29 Samples

Download data: BIGWIG, NARROWPEAK

Series

Accession:: GSE168002

ID:: 200168002

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Select item 2001680008.

Oct4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human [RNA-seq}

(Submitter supplied) Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their physical interactome in human ESCs (hESCs) has not been explored thus far. Here we mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
15 Samples

Download data: TXT

Series

Accession:: GSE168000

ID:: 200168000

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001679889.

Oct4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human [CUT&Tag]

(Submitter supplied) Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their physical interactome in human ESCs (hESCs) has not been explored thus far. Here we mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
3 Samples

Download data: BIGWIG, NARROWPEAK

Series

Accession:: GSE167988

ID:: 200167988

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Select item 20016797910.

Oct4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human [ATAC-seq]

(Submitter supplied) Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their physical interactome in human ESCs (hESCs) has not been explored thus far. Here we mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. more...

Organism:: Homo sapiens

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

Platform:: GPL18573
11 Samples

Download data: BIGWIG, NARROWPEAK

Series

Accession:: GSE167979

ID:: 200167979

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014775111.

OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human

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

Organism:: Homo sapiens

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

Platforms:: GPL21290 GPL20301 GPL18573
25 Samples

Download data: BED

Series

Accession:: GSE147751

ID:: 200147751

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Select item 20014775012.

OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human [RNA-Seq]

(Submitter supplied) Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). We mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. In naive hESCs, OCT4 is associated with both BRG1 and BRM, the two mutually exclusive ATPase subunits of the BAF complex. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
11 Samples

Download data: TSV

Series

Accession:: GSE147750

ID:: 200147750

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Select item 20014771613.

OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human [ChIP-Seq]

(Submitter supplied) Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). We mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. In naive hESCs, OCT4 is associated with both BRG1 and BRM, the two mutually exclusive ATPase subunits of the BAF complex. more...

Organism:: Homo sapiens

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

Platforms:: GPL20301 GPL18573
14 Samples

Download data: BED

Series

Accession:: GSE147716

ID:: 200147716

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Select item 20001646214.

Expression data from Chd1-deficient mouse ES cells (E14 cell lines) and genome-wide binding of Chd1 in parental ES cells

(Submitter supplied) We used microarrays to study the effect of Chd1 loss of function in mouse ES cells. We used ChIP-chip to analyze genome-wide binding of Chd1 in normal ES cells.

Organism:: Mus musculus

Type:: Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:: GPL6246 GPL7793
8 Samples

Download data: CEL, TXT

Series

Accession:: GSE16462

ID:: 200016462

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011222215.

BAZ2A safeguards genome architecture of ground-state pluripotent stem cells

(Submitter supplied) Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. more...

Organism:: Mus musculus

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

Platforms:: GPL21103 GPL19057 GPL17021
49 Samples

Download data: BED, BW, CSV, HIC

Series

Accession:: GSE112222

ID:: 200112222

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Select item 20009668816.

scMNase-seq measures chromatin accessibility and nucleosome positioning in single cells

(Submitter supplied) Nucleosome positioning is critical to chromatin accessibility, and is associated with gene expression programs in cells. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array surrounding the transcription start sites (TSSs ) of active genes and DNase I hypersensitive sites (DHSs). However, cells exhibit remarkable expression heterogeneity in response to active signaling even in a homogenous population of cells, which may be related to the heterogeneity in chromatin accessibility. more...

Organism:: Mus musculus

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

Platform:: GPL17021
586 Samples

Download data: BED

Series

Accession:: GSE96688

ID:: 200096688

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015448717.

Regulation of retrotransposon activity and telomeres in primed pluripotent stem cells (ChIP-seq)

(Submitter supplied) Naïve and primed pluripotent states represent two different states of pluripotency. Mouse naïve pluripotent stem cells (PSCs) exhibit germline competence as determined by chimera production test and can generate all-PSC mice by tetraploid embryo complementation (TEC) test, the most stringent functional test of developmental potency. By contrast, primed PSCs fail in germline chimeras and TEC test. Unfortunately, these tests cannot be applied to characterization of developmental pluripotency of human PSCs due to ethic issue. more...

Organism:: Mus musculus

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

Platform:: GPL21273
18 Samples

Download data: BW

Series

Accession:: GSE154487

ID:: 200154487

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014066718.

Regulation of retrotransposon activity and telomeres in primed pluripotent stem cells

(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

Platform:: GPL21273
27 Samples

Download data: BW

Series

Accession:: GSE140667

ID:: 200140667

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Select item 20014066519.

Regulation of retrotransposon activity and telomeres in primed pluripotent stem cells (RNA-seq)

(Submitter supplied) Naïve and primed pluripotent states represent two different states of pluripotency. Mouse naïve pluripotent stem cells (PSCs) exhibit germline competence as determined by chimera production test and can generate all-PSC mice by tetraploid embryo complementation (TEC) test, the most stringent functional test of developmental potency. By contrast, primed PSCs fail in germline chimeras and TEC test. Unfortunately, these tests cannot be applied to characterization of developmental pluripotency of human PSCs due to ethic issue. more...