GEO DataSets

(Submitter supplied) HP1 alpha, beta, and gamma play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, some HP1 family members may also participate in transcriptional regulation of genes. Recently, HP1 gamma binding to the bodies of a subset of genes has been observed in human and murine cells. However, the generality of this phenomenon and the role HP1 gamma may play in this context are unknown. more...

Organism:

Homo sapiens

Type:

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

8 related Platforms

39 Samples

Download data: BED, BEDGRAPH, GFF, GPR, PAIR

(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

Platform:

GPL13112

24 Samples

Download data: BED

(Submitter supplied) Cbx3 (HP1γ) that is a member of the heterochromatin protein 1 family play important roles in development and differentiation. To determine the regulatroy mechanisms of Cbx3 during neural differentiation from ESCs to NPCs, we performed RNA-seq analysis of ESCs or ESC-derived NPCs depleted for Cbx3 or Cbx3-assocatied Mediator subunit Med26.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: CSV

(Submitter supplied) Cbx3 (HP1γ) that is a member of the heterochromatin protein 1 familiy enriched in gene bodies of pluripotent ESCs but promoters of differentiated pre-iPSCs. To determine whether Cbx3 becomes enriched at promoters to influence gene regulation during differentiation, we converted ESCs to NPCs in monolayer culuture and performed genomewide ChIP-seq of Cbx3. Our results shows that Cbx3 enriches at the promoters of genes upon differentiation of ESCs to NPCs and stablizes the binding of Mediator subunit Med26 to pre-initiation complex (PIC) in NPCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

16 Samples

Download data: BED

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

27 Samples

Download data: BEDGRAPH, RPKM

(Submitter supplied) Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: BEDGRAPH, RPKM

(Submitter supplied) Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in pluripotency and development are largely unknown. Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: BEDGRAPH

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

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL8647 GPL18855

10 Samples

Download data: PAIR, TXT, WIG

(Submitter supplied) ChIP-chip of HPL-2 in hpl-2 C. elegans early embryo

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8647

1 Sample

Download data: PAIR, WIG

(Submitter supplied) ChIP-chip of HPL-2 in N2 C. elegans early embryo

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8647

3 Samples

Download data: PAIR, WIG

(Submitter supplied) ChIP-chip of HPL-2 in met-2 set-25 C. elegans mixed-stage embryo

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8647

2 Samples

Download data: PAIR, WIG

(Submitter supplied) Identification of genes significantly misregulated in hpl-2 mutant early embryo compared to wild-type early embryo

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL18855

4 Samples

Download data: PAIR, TXT

(Submitter supplied) mRNA expression levels were determined by NGS for wildtype larvae as well as for larvae lacking HP1a [Su(var)205^04/Su(var)205^05 transheterozygotes].

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

4 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6480 GPL9115

11 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

5 Samples

Download data: TXT

(Submitter supplied) Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

6 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing regulation involving chromatin, transcription and multiple protein factors. In particular, the CCCTC-binding factor (CTCF), the Argonaute protein AGO1, and members of heterochromatin protein 1 (HP1) family have been implicated in the regulation of splicing associated to chromatin and the elongation of RNAPII. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15106

6 Samples

Download data: CEL, CHP, XLS

(Submitter supplied) Heterochromatin is important for gene regulation and chromosome structure, but the genes that are occupied by heterochromatin proteins in the mammalian genome are largely unknown. We have adapted the DamID method to systematically identify target genes of the heterochromatin proteins HP1 and SUV39H1 in human and mouse cells. Unexpectedly, we found that HP1beta (CBX1) and SUV39H1 bind to genes encoding KRAB domain containing zinc finger (KRAB-ZNF) transcriptional repressors. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by genome tiling array

5 related Platforms

34 Samples

Download data: TIFF, TXT

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by genome tiling array

Platform:

GPL6629

23 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) In Drosophila, two chromosome-wide compensatory systems have been characterized; the dosage compensation system acting on the male X-chromosome and the chromosome specific regulation of genes located on the heterochromatic 4th chromosome. Dosage compensation in Drosophila is accomplished by hypertranscription of the single male X-chromosome mediated by the MSL-complex. The mechanism for this compensation is suggested to be an MSL-complex mediated enhanced transcriptional elongation while the mechanism for the compensation mediated by Painting of fourth (POF) on the 4th chromosome has remained elusive. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by genome tiling array

Platform:

GPL6629

5 Samples

Download data: CEL, CHP