GEO DataSets

(Submitter supplied) Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. more...

Organism:

Sulfolobus acidocaldarius; Sulfolobus islandicus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26275 GPL26274

31 Samples

Download data: TXT

(Submitter supplied) The three-dimensional organization of chromosomes can have a profound impact on their replication and expression. The chromosomes of higher eukaryotes possess discrete compartments that are characterized by differing transcriptional activities. Contrastingly, most bacterial chromosomes have simpler organization with local domains, the boundaries of which are influenced by gene expression. Numerous studies have revealed that the higher-order architectures of bacterial and eukaryotic chromosomes are dependent on the actions of Structural Maintenance of Chromosomes (SMC) superfamily protein complexes, in particular the near-universal condensin complex. more...

Organism:

Sulfolobus islandicus; Sulfolobus acidocaldarius

Type:

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

4 related Platforms

94 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) 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) Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically；chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16417

6 Samples

Download data: BED, BW

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL10448 GPL21273

28 Samples

Download data: BW, HIC, TXT

(Submitter supplied) Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL10448

4 Samples

Download data: TXT

(Submitter supplied) Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16417

10 Samples

Download data: BED, BW

(Submitter supplied) Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21273

4 Samples

Download data: HIC

(Submitter supplied) Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: TXT

(Submitter supplied) Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. more...

Organism:

Saccharolobus solfataricus P2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9463

8 Samples

Download data: TXT

(Submitter supplied) Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. more...

Organism:

Sulfolobus acidocaldarius

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23429 GPL23051

5 Samples

Download data: WIG

(Submitter supplied) TADs, CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL13304

18 Samples

Download data: BW, HIC

(Submitter supplied) Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher‐order organization remains elusive. Here, we investigate TAD higher‐order interactions with Hi‐C through neuronal differentiation and show that they form a hierarchy of domains‐within‐domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

6 Samples

Download data: TAR

(Submitter supplied) Eukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown that the DNA binding protein CTCF and cohesin contribute to a fraction of TAD boundaries. However, the relative importance of the role of epigenetic activity (like histone marks and transcription) over the genetic information (DNA sequence) in TAD formation is still not understood. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL23323 GPL19132

11 Samples

Download data: BEDGRAPH

(Submitter supplied) The discovery that genomes are partitioned into self-interacting modules or topologically associated domains (TADs) has revolutionized our understanding of the multiscale organization of chromatin. TADs are often considered as stable structures over time, however this view contrasts with the structural dynamics needed for DNA to cope rapidly and accurately with cell-specific and developmental programs regulation. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

3 Samples

Download data

(Submitter supplied) How genomic information is selectively utilized to direct spatial and temporal gene expression patterns during differentiation remains to be elucidated but it is clear that regulated changes in higher-order genomic architecture plays a fundamental role. Specifically, long range interactions within and between chromosomes and the position of chromosome territories in the nucleus are controlled by TADs and LADs respectively, but the relationship between these genomic organizers remains poorly understood

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL20301 GPL18573

34 Samples

Download data: BED, BW, FPKM_TRACKING, HIC

(Submitter supplied) Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs), and further down to sub-TAD loop domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) While mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. Here we generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

21 Samples

Download data: BROADPEAK, BW, TXT