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Links from GEO DataSets

Items: 20

1.

4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body

(Submitter supplied) Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
10 Samples
Download data: TXT
Series
Accession:
GSE184602
ID:
200184602
2.

4DNESB7XYI9V - sci-Hi-C on mESCs differentiated to embryoid body

(Submitter supplied) Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
6 Samples
Download data: TXT
3.

4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body

(Submitter supplied) Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
9 Samples
Download data: TXT
Series
Accession:
GSE184600
ID:
200184600
4.

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

(Submitter supplied) Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19057 GPL17021
25 Samples
Download data: TXT
Series
Accession:
GSE184554
ID:
200184554
5.

Structural organization of the inactive X chromosome

(Submitter supplied) X-chromosome inactivation (XCI) entails a massive structural reorganization of the inactive X (Xi). However the molecular architecture of the Xi is unknown. Here we show that the Xi lacks typical autosomal features such as active/inactive compartments and topologically associating domains (TADs), except around a small number of genes that escape XCI and remain expressed. Escaping genes form TADs and retain DNA accessibility at promoter-proximal and CTCF binding sites, indicating that these loci can avoid Xist-mediated erasure of chromosomal structure. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other; Third-party reanalysis
Platform:
GPL13112
8 Samples
Download data: TAR, TXT
Series
Accession:
GSE72697
ID:
200072697
6.

Allele-specific ATAC-seq

(Submitter supplied) One of the two X chromosomes in female somatic cells is transcriptionally silenced across cell generations, a classic paradigm of epigenetic regulation.  Although most genes are stably silenced, certain X-linked genes escape X-chromosome inactivation (XCI), providing a fundamental dosage difference between females and males.  A role for chromosome conformation has been proposed in XCI as the process is  accompanied by a massive structural reorganisation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
7 Samples
Download data: BW, NARROWPEAK, TXT
Series
Accession:
GSE71156
ID:
200071156
7.

Dynamics of gene silencing during X inactivation using allele-specific RNA-Seq

(Submitter supplied) Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL13112 GPL19057 GPL11002
20 Samples
Download data: BED, TXT, WIG
8.

Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [allele-specific analysis]

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
47 Samples
Download data: CSV
Series
Accession:
GSE184987
ID:
200184987
9.

Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation

(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:
GPL19057 GPL21103
727 Samples
Download data
Series
Accession:
GSE153847
ID:
200153847
10.

Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [smart-seq]

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
672 Samples
Download data: CSV, LOOM, XLSX
Series
Accession:
GSE153846
ID:
200153846
11.

Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [10X]

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
2 Samples
Download data: CSV
Series
Accession:
GSE153845
ID:
200153845
12.

Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [ATAC-seq]

(Submitter supplied) X chromosome reactivation (XCR) represents a paradigm to study epigenetic regulation and the reversal of chromatin silencing, although how it is linked to the pluripotency gene regulatory network, pluripotency transcription factors (TFs) and chromatin remodelling processes remains largely unexplained. Several pluripotency TFs have been linked to XCR through binding to the long non-coding RNA gene Xist, but whether other regulatory elements are involved is unclear. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: TXT
Series
Accession:
GSE153844
ID:
200153844
13.

An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [RNA-seq]

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...
Organism:
Mus musculus x Mus spretus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20213
17 Samples
Download data: TSV
Series
Accession:
GSE107291
ID:
200107291
14.

An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [ATAC-seq]

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...
Organism:
Mus musculus x Mus spretus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20213
4 Samples
Download data: BED, XLS
Series
Accession:
GSE107290
ID:
200107290
15.

An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [ChIP-seq]

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...
Organism:
Mus musculus x Mus spretus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20213
6 Samples
Download data: BED, XLS
Series
Accession:
GSE107286
ID:
200107286
16.

An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [DNase HiC]

(Submitter supplied) The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge, we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. more...
Organism:
Mus musculus x Mus spretus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20213
6 Samples
Download data: TXT
Series
Accession:
GSE107282
ID:
200107282
17.

Nucleophosmin binding on the mouse X chromosomes

(Submitter supplied) In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. Results We find radically different conformations for the two female mouse X chromosomes. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10129
2 Samples
Download data: GFF
Series
Accession:
GSE71903
ID:
200071903
18.

Bipartite structure of the inactive mouse X chromosome

(Submitter supplied) A subset of genomic regions, including one of the female X chromosomes and all imprinted genes, are expressed exclusively from a single allele in somatic cells of mammals. To evaluate structural changes associated with allelic silencing, we used mouse F1 hybrid systems in which X inactivation is skewed and alleles can be distinguished based on single nucleotide polymorphisms to analyze chromatin contacts by a new Hi-C assay that uses DNase I for chromatin fragmentation. more...
Organism:
Mus musculus x Mus spretus
Type:
Other
Platforms:
GPL20213 GPL16616
4 Samples
Download data: TXT
19.

Female-specific CTCF binding on the inactive X chromosome in mouse

(Submitter supplied) In mammals, genes located on the X chromosome are present in one copy in XY males and two in XX females. To balance the dosage of X-linked gene expression between the sexes one of the two X chromosomes in females is silenced by X inactivation initiated by up-regulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers for silencing. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. more...
Organism:
Mus musculus x Mus spretus; Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array
5 related Platforms
19 Samples
Download data: GFF, PAIR
Series
Accession:
GSE66262
ID:
200066262
20.

Effects of Firre knockdown on mouse gene expression

(Submitter supplied) In mammals, genes located on the X chromosome are present in one copy in XY males and two in XX females. To balance the dosage of X-linked gene expression between the sexes one of the two X chromosomes in females is silenced by X inactivation initiated by up-regulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers for silencing. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus. more...
Organism:
Mus musculus x Mus spretus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16617
4 Samples
Download data: TXT
Series
Accession:
GSE66172
ID:
200066172
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