GEO DataSets

(Submitter supplied) We sequenced mRNA from wild type and Hst1 knock out strains of Candida lusitaniae to generate the gene expression profiles and studied the differentially expressed genes between the two conditions.

Organism:

Clavispora lusitaniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20764

6 Samples

Download data: TXT

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

Organism:

Clavispora lusitaniae

Type:

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

Platforms:

GPL20764 GPL20765

10 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) The goal of this study is to identifiy centromere locations of Candida lusitaniae through ChIP-Seq analysis. We applied ChIP-Seq on two centromere proteins: Cse4 and Mif2. After peak calling, we identified one peak in each of the 8 supercontigs of Candida lusitaniae which may represent the potential centromere location.

Organism:

Clavispora lusitaniae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20765

4 Samples

Download data: NARROWPEAK

(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) We use high-resolution chemical cleavage mapping and both native and cross-linked chromatin immunoprecipitation with paired-end sequencing to elucidate the profile of nuceleosomes containing the centromere-specific variant of H3 (cenH3), known as CENP-A or Cnp1 in fission yeast. We find that in the central domain of fission yeast centromeres H3 nucleosomes are nearly absent and CENP-A nucleosomes are more widely spaced that nucleosomes elsewere. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

41 Samples

Download data: BED, WIG

(Submitter supplied) Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30973

16 Samples

Download data: BAM, BW, TSV

(Submitter supplied) Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. more...

Organism:

Homo sapiens; Cricetulus griseus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31911

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. more...

Organism:

Cricetulus griseus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31910

8 Samples

Download data: BW

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

Organism:

Cricetulus griseus; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by high throughput sequencing

4 related Platforms

68 Samples

Download data: TXT

(Submitter supplied) This study was designed to investigate the chromatin structure of human centromeres. Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. more...

Organism:

Cricetulus griseus; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL31868 GPL31869

39 Samples

Download data: TXT

(Submitter supplied) This study was designed to investigate the chromatin structure of human centromeres. Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. more...

Organism:

Cricetulus griseus; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL31869

7 Samples

Download data: TXT

(Submitter supplied) This study was designed to investigate the chromatin structure of human centromeres. Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. more...

Organism:

Cricetulus griseus; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL31868 GPL31869

10 Samples

Download data: TXT

(Submitter supplied) Specification and propagation of the centromeres of eukaryotic chromosomes is determined by epigenetic mechanisms. Unfortunately, the epigenetic characteristics of centromeric DNA and chromatin are difficult to define because the centromeres are composed of highly repetitive DNA sequences in most eukaryotic species. Several rice centromeres have been fully sequenced, making rice an excellent model for centromere research. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9147

1 Sample

Download data: TXT

(Submitter supplied) ChIP Seq revealed presence of unique CEN-proximal neocentromere peaks in CEN deleted clones. Using 10 million reads generated from ChIP-seq for each sample, chromosome wide maps for CENP-A enrichment were generated .

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15149

14 Samples

Download data: BED

(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) In order to address the replication timing of the centromeres in yeast Candida albicans, we have determined at high temporal and spatial resolution its genome-wide DNA replication timing profile. This was done by sorting S- and G1-phase cells by FACS and hybridizing DNA from both fractions onto genomic tiling arrays. Data was normalized, organized by chromosomal positition, and smoothed. Replication timing is inferred from the DNA copy number along the chromosome with data peaks corresponding to predicted origins of DNA replication. more...

Organism:

Candida albicans

Type:

Other

Platforms:

GPL9148 GPL9150

6 Samples

Download data: SRR, TXT

(Submitter supplied) We report the effects of overexpression of ZFAT on mRNA profiles in HT1080 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: TAB

(Submitter supplied) ZFAT is a nuclear protein that harbors putative DNA-binding domains. Studies in mice have shown that ZFAT plays a critical role in survival and differentiation in T cells. However, molecular mechanisms whereby ZFAT regulates gene expression programs in human cells remain poorly unknown. We here identify the direct target genes of ZFAT in HEK293 human embryonic kidney cells through combination of chromatin immunoprecipitation with sequencing and transcriptional profiling.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18460

2 Samples

Download data: NARROWPEAK

(Submitter supplied) Investigation of centromeres in the pathogenic yeast Candida parapsilosis, shows that the location of two centromeres are polymorphic within this species. The centromeres consist of large inverted repeats (IRs), surrounding unique sequences. New (neo) centromeres have emerged in one C. parapsilosis isolate even though the original CEN location is undamaged. The neocentromeres do not contain IRs, and have no obvious sequence features.

Organism:

Candida parapsilosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27421

10 Samples

Download data: BIGWIG