GEO DataSets

(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) 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) 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 T cells remain poorly unknown. We here identify the direct target genes of ZFAT in thymocytes through combination of chromatin immunoprecipitation with sequencing and transcriptional profiling.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

12 Samples

Download data: TXT

(Submitter supplied) RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been difficult to detect in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

72 Samples

Download data: TXT

(Submitter supplied) Centromere is the chromosomal locus at which kinetochore is assembled to direct chromosome segregation. Histone H3 variant CENP-A epigenetically marks active centromeres; however, the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, we find that CENP-ACnp1 chromatin assembly at the centromere requires the Ino80 ATP-dependent chromatin remodeling complex which removes histone H3-containing nucleosomes from associated chromatin. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

98 Samples

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(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) 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:

Oryza sativa

Type:

Expression profiling by MPSS

Platforms:

GPL3776 GPL3777

2 Samples

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(Submitter supplied) The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platform:

GPL3777

1 Sample

Download data

(Submitter supplied) The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platform:

GPL3776

1 Sample

Download data

(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