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Links from GEO DataSets

Items: 20

1.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [Hi-C]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
2 Samples
Download data: TXT
2.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin

(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; Other
Platform:
GPL17021
42 Samples
Download data: BW, TXT
Series
Accession:
GSE166041
ID:
200166041
3.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [scRNA-seq]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: CSV
Series
Accession:
GSE166027
ID:
200166027
4.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [RNA-seq]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
12 Samples
Download data: XLSX
Series
Accession:
GSE166025
ID:
200166025
5.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ChIP-seq]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
18 Samples
Download data: BW
Series
Accession:
GSE166023
ID:
200166023
6.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ATAC-seq]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
2 Samples
Download data: BW
Series
Accession:
GSE166022
ID:
200166022
7.

Global analysis of gene expression changes following LINE1 inhibition [III]

(Submitter supplied) Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
12 Samples
Download data: XLSX
Series
Accession:
GSE111633
ID:
200111633
8.

Global analysis of gene expression changes following LINE1 inhibition

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21103 GPL17021
33 Samples
Download data
Series
Accession:
GSE100939
ID:
200100939
9.

Global analysis of gene expression changes following LINE1 inhibition [II]

(Submitter supplied) Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
15 Samples
Download data: XLSX
Series
Accession:
GSE100938
ID:
200100938
10.

Global analysis of gene expression changes following LINE1 inhibition [I]

(Submitter supplied) Transposable elements make up nearly half of mammalian genomes, yet are generally described as ‘junk DNA’ or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: XLSX
Series
Accession:
GSE100937
ID:
200100937
11.

NELFA is a novel regulator of the 2C-like state

(Submitter supplied) Mouse embryonic stem cells (mESCs) are not homogenous; a rare subpopulation of cells can sporadically transit into a early-embryonic-like state and exhibits a gene expression program resembling that of the 2-cell (2C) embryo. We identified the maternal factor NELFA as a novel driver of the 2C-like gene expression through multiple mechanisms. We further demonstrate that the entry of mESCs into the 2C-like state is accompanied by epigenetic and metabolic reprogramming, and that perturbation of the metabolic state via a small molecule can promote this cell fate reversion in a NELFA-dependent manner, obviating the need for any genetic manipulation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21103 GPL19057
35 Samples
Download data: BW, NARROWPEAK, XLSX
Series
Accession:
GSE113671
ID:
200113671
12.

Transcription profile of FBL-knock down ES cells

(Submitter supplied) Pluripotent stem cells have been shown to have unique nuclear properties, e.g., hyperdynamic chromatin and large, condensed nucleoli. However, the contribution of the latter unique nucleolar character to pluripotency has not been well understood. Here, we show fibrillarin (FBL), a critical methyltransferase for ribosomal RNA (rRNA) processing in nucleoli, as one of the proteins highly expressed in pluripotent embryonic stem (ES) cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
4 Samples
Download data: TXT
Series
Accession:
GSE51139
ID:
200051139
13.

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
14.

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
15.

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
16.

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
17.

Surveillance of rRNA synthesis by an RNA helicase mediates tissue-specific developmental disorders

(Submitter supplied) Myriad of craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as ribosome biogenesis. While it is understood that many of these highly tissue-specific malformations are a consequence of defects in cranial neural crest cells (cNCCs), an embryonic cell group that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell type-selectivity of these effects remains largely unknown. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL18573 GPL16791
10 Samples
Download data: BW, WIG
Series
Accession:
GSE89420
ID:
200089420
18.

RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (ChIP-Seq 3)

(Submitter supplied) N6-methyladenosine (m6A) methyltransferase METTL3 mainly mediates mRNA m6A methylation and plays important roles in various biological processes. Here we report a chromatin-based role for METTL3 in heterochromatin integrity regulation in mouse embryonic stem cells (mESCs). We show that in mESCs METTL3 predominantly localizes to one of the most active endogenous retroviruses (ERVs) families, the intracisternal A-type particles (IAPs). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21273
4 Samples
Download data: BW
Series
Accession:
GSE160103
ID:
200160103
19.

RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-Seq 2)

(Submitter supplied) N6-methyladenosine (m6A) methyltransferase METTL3 mainly mediates mRNA m6A methylation and plays important roles in various biological processes. Here we report a chromatin-based role for METTL3 in heterochromatin integrity regulation in mouse embryonic stem cells (mESCs). We show that in mESCs METTL3 predominantly localizes to one of the most active endogenous retroviruses (ERVs) families, the intracisternal A-type particles (IAPs). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21273
6 Samples
Download data: BW
Series
Accession:
GSE154139
ID:
200154139
20.

RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (MeRIP-Seq)

(Submitter supplied) N6-methyladenosine (m6A) methyltransferase METTL3 mainly mediates mRNA m6A methylation and plays important roles in various biological processes. Here we report a chromatin-based role for METTL3 in heterochromatin integrity regulation in mouse embryonic stem cells (mESCs). We show that in mESCs METTL3 predominantly localizes to one of the most active endogenous retroviruses (ERVs) families, the intracisternal A-type particles (IAPs). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL21273
12 Samples
Download data: BW
Series
Accession:
GSE154138
ID:
200154138
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