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Items: 1 to 20 of 184

1.

TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

(Submitter supplied) Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. more...
Organism:
Mus musculus; Mus pahari; Hylobates moloch; Macaca mulatta; Homo sapiens; Mus caroli; Rattus norvegicus; Nomascus leucogenys
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
9 related Platforms
85 Samples
Download data: BED, BEDGRAPH, BIGWIG, BW, COOL, XLSX
Series
Accession:
GSE197926
ID:
200197926
2.

Conservation of chromatin organization within human and primate centromeres

(Submitter supplied) The focal attachment of the kinetochore to the centromere core is essential for genome maintenance, yet the highly repetitive nature of human centromeres limits our understanding of their chromatin organization. We demonstrate that single-molecule chromatin fiber sequencing can uniquely resolve chromatin organization within centromeres at single-molecule and single-nucleotide resolution. We find that the centromere core contains a dichotomous chromatin organization not found elsewhere in the genome, which is characterized by highly accessible chromatin patches heterogeneously punctuated amongst tightly compacted nucleosome arrays. more...
Organism:
Homo sapiens; Hoolock leuconedys
Type:
Other
Platforms:
GPL28352 GPL33203
4 Samples
Download data: BED, FA
Series
Accession:
GSE226394
ID:
200226394
3.

Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [ChIP-seq]

(Submitter supplied) Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. more...
Organism:
Hylobates moloch; Hoolock leuconedys; Nomascus leucogenys; Symphalangus syndactylus
Type:
Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
22 Samples
Download data: FA, TXT, XLSX
Series
Accession:
GSE161308
ID:
200161308
4.

Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Hylobates moloch; Hoolock leuconedys; Nomascus leucogenys; Symphalangus syndactylus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
26 Samples
Download data: FA, TXT
Series
Accession:
GSE161217
ID:
200161217
5.

Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [RNA-seq]

(Submitter supplied) Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. more...
Organism:
Symphalangus syndactylus; Nomascus leucogenys; Hylobates moloch; Hoolock leuconedys
Type:
Expression profiling by high throughput sequencing
4 related Platforms
4 Samples
Download data: TXT
Series
Accession:
GSE161191
ID:
200161191
6.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Symphalangus syndactylus; Hylobates lar; Hylobates muelleri; Nomascus gabriellae; Nomascus leucogenys; Hylobates moloch; Hylobates pileatus; Hoolock leuconedys
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
15 related Platforms
60 Samples
Download data: TXT
Series
Accession:
GSE136968
ID:
200136968
7.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [WGS]

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...
Organism:
Symphalangus syndactylus; Nomascus gabriellae; Hylobates lar; Hylobates pileatus; Nomascus leucogenys; Hylobates muelleri; Hylobates moloch; Hoolock leuconedys
Type:
Other
14 related Platforms
23 Samples
Download data: XLSX
Series
Accession:
GSE136966
ID:
200136966
8.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome[RNA-Seq]

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...
Organism:
Nomascus leucogenys
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL25055 GPL24727
9 Samples
Download data: TXT
Series
Accession:
GSE136965
ID:
200136965
9.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [PU.1 ChIP-seq]

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...
Organism:
Nomascus leucogenys
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27430
4 Samples
Download data: BEDGRAPH, TXT, XLSX
Series
Accession:
GSE136964
ID:
200136964
10.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [Histone ChIP-seq]

(Submitter supplied) Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. more...
Organism:
Nomascus leucogenys
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL25055 GPL24727
24 Samples
Download data: BEDGRAPH
Series
Accession:
GSE136963
ID:
200136963
11.

Continuous-trait probabilistic model for comparing multi-species functional genomic data

(Submitter supplied) We developed a probabilistic method to simultaneously infer genome-wide heterogeneous evolutionary states. We applied the proposed method to analyze a cross-species DNA replication timing (RT) dataset from the same cell type in five primate species. We demonstrated that the proposed model enables discovery of genomic regions with distinct evolutionary patterns of RT.
Organism:
Nomascus leucogenys; Chlorocebus aethiops; Homo sapiens; Pan troglodytes; Pongo pygmaeus
Type:
Other
5 related Platforms
5 Samples
Download data: BW
Series
Accession:
GSE111733
ID:
200111733
12.

Human-specific features of special gene expression and regulation in eight brain regions

(Submitter supplied) Despite the substantial efforts made to compile the molecular maps of the human brain, they do not fully inform us of the features unique to humans. Yet, identification of these features might help us to understand both the evolution and nature of the human cognitive traits. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, gibbon and macaques. more...
Organism:
Homo sapiens; Hylobates lar; Gorilla gorilla; Pan troglodytes
Type:
Expression profiling by high throughput sequencing
7 related Platforms
107 Samples
Download data: TXT
Series
Accession:
GSE100796
ID:
200100796
13.

Epigenetic maintenance of topological domains in the rearranged gibbon genome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Macaca mulatta; Nomascus leucogenys
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL14954 GPL25056 GPL25055
6 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE115065
ID:
200115065
14.

Epigenetic maintenance of topological domains in the rearranged gibbon genome [ChIP-seq]

(Submitter supplied) The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. more...
Organism:
Nomascus leucogenys
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL25055
3 Samples
Download data: BW
Series
Accession:
GSE115064
ID:
200115064
15.

Epigenetic maintenance of topological domains in the rearranged gibbon genome [WBGS]

(Submitter supplied) The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. more...
Organism:
Nomascus leucogenys; Macaca mulatta
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL14954 GPL25056
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE115063
ID:
200115063
16.

Epigenetic maintenance of topological domains in the rearranged gibbon genome [Hi-C]

(Submitter supplied) The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. more...
Organism:
Nomascus leucogenys
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL25055
1 Sample
Download data: BED
Series
Accession:
GSE115062
ID:
200115062
17.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Hoolock leuconedys; Macaca mulatta; Pan troglodytes; Homo sapiens; Macaca; Macaca fascicularis
Type:
Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
6 related Platforms
86 Samples
Download data
Series
Accession:
GSE85868
ID:
200085868
18.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [SNP]

(Submitter supplied) We report the application of DNA sequencing technology for high-throughput sequencing of mix candidate genes' PCR products totally 38 based on DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues.
Organism:
Homo sapiens; Pan troglodytes; Macaca; Macaca fascicularis; Hoolock leuconedys
Type:
Genome variation profiling by high throughput sequencing
5 related Platforms
48 Samples
Download data: VCF
Series
Accession:
GSE85867
ID:
200085867
19.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [methylation]

(Submitter supplied) We report the application of DNA sequencing technology for high-throughput sequencing of mix bis-PCR products totally 38 based on bisulfate treated DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues.
Organism:
Hoolock leuconedys; Macaca fascicularis; Pan troglodytes; Homo sapiens; Macaca mulatta
Type:
Methylation profiling by high throughput sequencing
5 related Platforms
38 Samples
Download data: TXT
Series
Accession:
GSE76788
ID:
200076788
20.

Array-Painting with Hoolock sorted chromosomes

(Submitter supplied) Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH and selective sequencing in two of the four karyomorphs, has shown that high resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. more...
Organism:
Hoolock leuconedys; Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL15909
5 Samples
Download data: TXT
Series
Accession:
GSE40024
ID:
200040024
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