GEO DataSets

(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) 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

(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:

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

(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

(Submitter supplied) Recent advances enabled by Hi-C technique have unraveled principles of chromosomal folding, which were since linked to many genomic processes. In particular, Hi-C revealed that chromosomes of animals are organized into Topologically Associating Domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. However, mechanisms that underlie partitioning of the genome into TADs remain poorly understood. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17275 GPL13304

20 Samples

Download data: TXT, VCF

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL11154

22 Samples

Download data: BED

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: TSV

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform HiC chromosome conformation, ChIP-seq and RNA-seq to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BED

(Submitter supplied) A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type specific gene expression profiles. Here, we perform Hi-C chromosome conformation to investigate how the three-dimensional organization of the cancer genome is disrupted in the context of epigenetic remodelling and atypical gene expression programs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

13 Samples

Download data: BED, TXT

(Submitter supplied) Gene activity programmes in different cell types control development and homeostasis of multi-cellular organisms. Spatial genome organization controls gene activity by facilitating or restricting contacts between gene promoters and remote gene enhancers. Functionally related co-regulated genes are often located together in genomes loci. The spatial organization of very large co-regulated gene loci remains poorly understood. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) We profiled replication timing in Suz12 knockout ESCs and observed no differences relative to wild-type controls.

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11620

2 Samples

Download data: PAIR

(Submitter supplied) Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

25 related Platforms

993 Samples

Download data: BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, PAIR, TSV, TXT

(Submitter supplied) Three-dimensional genome structure plays an important role in gene regulation. Globally chromosomes are organized into active and inactive compartments, while at the gene level looping interactions connect promoters to regulatory elements. Topologically Associating Domains (TADs), typically several hundred kilobases in size form an intermediate level of organization. Major questions include how TADs are formed and what their relation is with looping interactions between genes and regulatory elements. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL10999

10 Samples

Download data: MATRIX, PNG, TXT, ZIP

(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

(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

(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

(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

(Submitter supplied) Upon fertilization, drastic chromatin reorganization occurs during human preimplantation development. However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored. Deciphering such process is crucial for understanding both early human development and in vitro fertilization. Here, we investigated genome-wide chromatin accessibility in human preimplantation embryos by employing an improved ATAC-seq that uses as few as 20 cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154 GPL16791

55 Samples

Download data: BED, TXT, WIG

(Submitter supplied) The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. more...

Organism:

Homo sapiens

Type:

Other; Third-party reanalysis

Platform:

GPL16791

38 Samples

Download data: BW, MAT