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Links from GEO DataSets

Items: 20

1.

A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [ChIP-Seq]

(Submitter supplied) The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21103 GPL17021
13 Samples
Download data: BEDGRAPH, NARROWPEAK
Series
Accession:
GSE101714
ID:
200101714
2.

Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes

(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
Platforms:
GPL21103 GPL17021
30 Samples
Download data: BEDGRAPH
Series
Accession:
GSE129427
ID:
200129427
3.

Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [4C-seq]

(Submitter supplied) The spatial organization of the mammalian genome is complex and relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains are largely determined by bound CTCF molecules and often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases such domains may act as coherent regulatory units, with a global on or off state. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
6 Samples
Download data: BEDGRAPH
Series
Accession:
GSE129426
ID:
200129426
4.

Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [ChIP-seq]

(Submitter supplied) The spatial organization of the mammalian genome is complex and relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains are largely determined by bound CTCF molecules and often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases such domains may act as coherent regulatory units, with a global on or off state. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21103 GPL17021
16 Samples
Download data: BEDGRAPH
Series
Accession:
GSE129425
ID:
200129425
5.

Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [RNA-seq]

(Submitter supplied) The spatial organization of the mammalian genome is complex and relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains are largely determined by bound CTCF molecules and often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases such domains may act as coherent regulatory units, with a global on or off state. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: BEDGRAPH
Series
Accession:
GSE129424
ID:
200129424
6.

A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21103 GPL17021
91 Samples
Download data: BEDGRAPH, MATRIX, NARROWPEAK, TAR, TXT
Series
Accession:
GSE101717
ID:
200101717
7.

A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]

(Submitter supplied) The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. more...
Organism:
Mus musculus
Type:
Other; Third-party reanalysis
Platform:
GPL21103
6 Samples
Download data: MATRIX, TAR, TXT
Series
Accession:
GSE101715
ID:
200101715
8.

A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [4C-Seq]

(Submitter supplied) The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
72 Samples
Download data: BEDGRAPH
Series
Accession:
GSE101713
ID:
200101713
9.

Chromatin topology and the timing of enhancer function at the HoxD locus

(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
Platforms:
GPL21103 GPL17021
72 Samples
Download data: BEDGRAPH, BW
Series
Accession:
GSE154189
ID:
200154189
10.

Chromatin topology and the timing of enhancer function at the HoxD locus [RNA-seq]

(Submitter supplied) The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate separately from two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory sub-modules. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
4 Samples
Download data: BEDGRAPH
Series
Accession:
GSE154188
ID:
200154188
11.

Chromatin topology and the timing of enhancer function at the HoxD locus [ChIP-seq]

(Submitter supplied) The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate separately from two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory sub-modules. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21103
9 Samples
Download data: BEDGRAPH
Series
Accession:
GSE154187
ID:
200154187
12.

Chromatin topology and the timing of enhancer function at the HoxD locus [4C-seq]

(Submitter supplied) In tetrapods, the HoxD gene cluster is critical for proper limb formation. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations emanate from the two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several regulatory elements controlling Hoxd genes, initially in a temporal manner and then in the proximal presumptive forearm. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
59 Samples
Download data: BEDGRAPH, BW, COOL
Series
Accession:
GSE154186
ID:
200154186
13.

Large-scale genomic reorganizations of topological domains (TADs) at the HoxD locus (4C-Seq)

(Submitter supplied) The transcriptional activation of Hoxd genes during mammalian limb development involves dynamic interactions with the two Topologically Associating Domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior Hoxd genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
12 Samples
Download data: BEDGRAPH
Series
Accession:
GSE98861
ID:
200098861
14.

Large-scale genomic reorganizations of topological domains (TADs) at the HoxD locus

(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
15 Samples
Download data: BEDGRAPH, BW
Series
Accession:
GSE98233
ID:
200098233
15.

Analysis of gene expression in the distal forelimbs in 2.4Mb inversion adjacent to the HoxD cluster

(Submitter supplied) E12.5 mouse distal forelimb embryonic transcriptome
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
2 Samples
Download data: BW, TXT
Series
Accession:
GSE98232
ID:
200098232
16.

ChIP-seq analysis of CTCF in distal limbs at mouse E12.5 using anti-CTCF

(Submitter supplied) We performed ChIP-seq for CTCF using the autopod from E12.5 embryo and confirmed the binding pattern previously reported by a ChIP-on-Chip approach using the same embryonic tissue (Soshnikova et al., 2010). Our results show CTCF-mediated gating of long-range contacts at the HoxD locus.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
1 Sample
Download data: BW
Series
Accession:
GSE96558
ID:
200096558
17.

A complex regulatory landscape involved in the development of external genitals

(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
Platforms:
GPL21103 GPL17021 GPL19057
65 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE138514
ID:
200138514
18.

A complex regulatory landscape involved in the development of external genitals [ATAC-Seq]

(Submitter supplied) In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we use a TAD flanking the HoxD gene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
15 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE138513
ID:
200138513
19.

A complex regulatory landscape involved in the development of external genitals [RNA-Seq]

(Submitter supplied) In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we use a TAD flanking the HoxD gene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
4 Samples
Download data: BEDGRAPH
Series
Accession:
GSE138511
ID:
200138511
20.

A complex regulatory landscape involved in the development of external genitals [CnR]

(Submitter supplied) In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we use a TAD flanking the HoxD gene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
3 Samples
Download data: BEDGRAPH
Series
Accession:
GSE138510
ID:
200138510
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db=gds|term=|query=1|qty=2|blobid=MCID_66740402ccfbad768f7bdf35|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
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