GEO DataSets

(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:

Macaca mulatta; Homo sapiens; Mus musculus; Mus pahari; Hylobates moloch; 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

(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

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

Organism:

Nomascus leucogenys; Hylobates moloch; Hoolock leuconedys; 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

(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

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

Organism:

Hylobates lar; Hylobates muelleri; Nomascus gabriellae; Nomascus leucogenys; Symphalangus syndactylus; 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

(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:

Hylobates lar; Hylobates pileatus; Nomascus leucogenys; Symphalangus syndactylus; Nomascus gabriellae; Hylobates muelleri; Hylobates moloch; Hoolock leuconedys

Type:

Other

14 related Platforms

23 Samples

Download data: XLSX

(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

(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

(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:

GPL24727 GPL25055

24 Samples

Download data: BEDGRAPH

(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

(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:

GPL25055 GPL14954 GPL25056

6 Samples

Download data: BED, BEDGRAPH

(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

(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:

Macaca mulatta; Nomascus leucogenys

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25056 GPL14954

2 Samples

Download data: BEDGRAPH

(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