GEO DataSets

(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:

Nomascus leucogenys; Symphalangus syndactylus; Hylobates moloch; Hoolock leuconedys

Type:

Expression profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: 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:

Nomascus leucogenys; Hylobates moloch; Hoolock leuconedys; 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:

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

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

Organism:

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

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

(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:

GPL25055 GPL24727

24 Samples

Download data: BEDGRAPH

(Submitter supplied) Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats, often 100-400 bp in length, found on every chromosome, typically in one location within heterochromatin. more...

Organism:

Drosophila melanogaster; Drosophila simulans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17275 GPL22293

19 Samples

Download data: FASTA, RTF

(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

(Submitter supplied) Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify. Here, we describe centromeres in the model oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). more...

Organism:

Phytophthora sojae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25217

3 Samples

Download data: BW

(Submitter supplied) Centromeres play an essential role in cell division by specifying the site of kinetochore formation on each chromosome so that chromosomes can attach to the mitotic spindle for segregation. Centromeres are defined epigenetically by the histone  H3 variant CEntromere Protein A (CENP-A). Dividing cells maintain the centromere  by depositing new CENP-A each cell cycle to replenish CENP-A diluted by replication. more...

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22393 GPL22426

15 Samples

Download data: BED, BW, FA

(Submitter supplied) Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. more...

Organism:

Triticum aestivum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17701

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Centromeric repetitive DNA sequences are highly variable during evolution, which are the hub for genome stability in almost all the eukaryotic organisms. However, how centromeric repeat sequences diverge rapidly among closely related species and populations, and how polyploidy contributed to the diversity of centromere among co-evolved subgenomes are largely unknown. Here, we applied the Brachypodium system to investigate the track of centromere evolution within this taxa, and their adaptation to alloploidization process. more...

Organism:

Brachypodium hybridum; Brachypodium stacei; Brachypodium distachyon

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL29084 GPL17337 GPL29083

12 Samples

Download data: BED

(Submitter supplied) Using high-resolution chromatin immunoprecipitation (ChIP) of centromere components and clustering of sequence data we find that specific dimeric alpha-satellite units shared by multiple individuals dominate functional human centromeres.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

19 Samples

Download data

(Submitter supplied) Pneumocystis is a relevant genetic system to study centromere formation in relation with host adaptation. How centromeres are formed and maintained in strongly host adapted fungal pathogens is poorly investigated. Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. more...

Organism:

Pneumocystis carinii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33206

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Pneumocystis is a relevant genetic system to study centromere formation in relation with host adaptation. How centromeres are formed and maintained in strongly host adapted fungal pathogens is poorly investigated. Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. more...

Organism:

Pneumocystis carinii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33206

4 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) The proteasome is a central player in several cellular aspects, such as homeostasis, cell cycle progression, and even transcription. Recent work has shown that proteasome inhibition promotes pervasive epigenetic changes in the human genome. However, the impact of proteasome inhibitors on ncRNAs is poorly understood. We treated control (asynchronous) or G2-synchronized HCT-116 human colon cancer cells with the proteasome inhibitors MG132 and bortezomib and performed total RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: TSV

(Submitter supplied) Following cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell. Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of the transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

20 Samples

Download data: BED

(Submitter supplied) Aberrant transcription of the HSATII pericentromeric satellite repeat is present in a wide variety of epithelial cancers. We observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under non-adherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generate complementary DNA intermediates in the form of DNA:RNA hybrids. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL14761

6 Samples

Download data: XLS