GEO DataSets

Analysis of embryonic fibroblasts depleted of the polycomb group (PcG) proteins EZH2, EED, SUZ12, or BMI-1. PcG proteins form complexes that regulate the expression of homeotic genes during development. Results provide insight into the mechanisms employed by PcGs to control development.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 5 protocol sets

Platform:

GPL96

Series:

GSE6015

15 Samples

Download data: CEL

(Submitter supplied) The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer. Here, we identify their target genes using genome-wide location analysis in human embryonic fibroblasts. We find that Polycomb-Repressive Complex 1 (PRC1), PRC2, and tri-methylated histone H3K27 co-occupy >1000 silenced genes with a strong functional bias for embryonic development and cell fate decisions. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2445

Platform:

GPL96

15 Samples

Download data: CEL

(Submitter supplied) Polycomb group (PcG) proteins form multiprotein complexes, called Polycomb repressive complexes (PRCs). PRC2 contains the PcG proteins EZH2, SUZ12, and EED and represses transcription through methylation of lysine (K) 27 of histone H3 (H3). Suz12 is essential for PRC2 activity and its inactivation results in early lethality of mouse embryos.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

(Submitter supplied) Polycomb repressive complex 2 (PRC2) trimethylates lysine 27 of histone H3 (H3K27me3), which regulates gene expression and controls diverse biological transitions in development, embryonic stem cell (ESC) differentiation, and cancer. Here we show that Polycomb-like 3 (Pcl3) is a component of PRC2 that promotes H3K27 trimethylation in ESCs. Chromatin immunoprecipitation and sequencing (ChIP-seq) revealed that Pcl3 co-localizes and recruits Suz12 to CpG islands. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

10 Samples

Download data: BAM, BED

(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we used a mouse model of T-ALL through the overexpression of the intarcellular transcriptionally active part of Notch1 (N1-IC). This model faithfully recapitulates the major characteristics of the human disease. Comparison of the leukemic cells from peripheral tumors(thymoma) of this mouse model to normal thymic cells Double Positive (DP) for the markers CD4 and CD8 that express very low levels of Notch1 showed major expression changes (please see GSE34554) in pathways controlling the transition from physiology to disease. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

18 Samples

Download data: BED

(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we used a mouse model of T-ALL through the overexpression of the intarcellular transcriptionally active part of Notch1 (N1-IC). This model faithfully recapitulates the major characteristics of the human disease. Comparison of the leukemic cells from peripheral tumors(thymoma) of this mouse model to normal thymic cells Double Positive (DP) for the markers CD4 and CD8 that express very low levels of Notch1 showed major expression changes in pathways controlling the transition from physiology to disease. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4303

Platform:

GPL1261

4 Samples

Download data: CEL

Analysis of DP (CD4+/8+) cells from an intracellular Notch1 (Notch1-IC)-induced T-ALL model that recapitulates most features of human T-ALL. T-ALL malignancy is driven by oncogenic activation of NOTCH1 signaling. Results provide insight into the molecular basis of Notch1-driven leukemogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL1261

Series:

GSE34554

4 Samples

Download data: CEL

(Submitter supplied) The core Polycomb Repressor Complex 2 (PRC2) is composed of Ezh1/2, Suz12, Eed and is responsible for mediating both H3K27me2 and H3K27me3. However, the mechanisms by which PRC2 demarcates these two repressive modifications in the genome are unknown. In a functional screen, we identified the H3K36 dimethyltransferase Nsd1 as a modulator of PRC2-mediated di- and trimethylation of H3K27. ChIP-Seq analysis following the depletion of Nsd1 revealed a global reduction in H3K36me2 and an increase in H3K27me3 at sites previously marked by H3K27me2. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

9 Samples

Download data: BW

(Submitter supplied) The polycomb group (PcG) proteins function in gene silencing through histone modifications. They form chromatin-associated multiprotein complexes, termed polycomb repressive complex (PRC) 1 and PRC2. These two complexes work in a coordinated manner in the maintenance of cellular memories through transcriptional repression of target genes. EZH2 is a catalytic component of PRC2 and trimethylates histone H3 at lysine 27 to transcriptionally repress the target genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

4 Samples

Download data: TXT

(Submitter supplied) For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3793

14 Samples

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(Submitter supplied) Suz12 samples are biological replicates from F9 cells crosslinked on different days. EZH2 and H3me3K27 samples are from the same batch of crosslinked cells as Suz12 replicate 2. For each sample matched total was prepared in parallel. Amplicons were made and hybridized on custom genomic tiling arrays. Keywords: ChIP-chip

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3794

4 Samples

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(Submitter supplied) For each sample a matched total was produced in parallel. Amplicons were made from each and hybridized on human 5.0 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3791

3 Samples

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(Submitter supplied) These samples are biological replicates from Ntera cells that were crosslinked on different days. For each sample a matched total was produced in a parallel. Amplicons were made from each and hybridized on human 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3787

4 Samples

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(Submitter supplied) All samples are from the same batch of crosslinked Ntera cells with a matched total produced in parallel. Amplicons were made from each and hybridized on ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3792

4 Samples

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4133 GPL10332

27 Samples

Download data: TXT

(Submitter supplied) Human epidermal stem cells transit from a slow cycling to an actively proliferating state to contribute to homeostasis. Both stem cell states differ in their cell cycle profiles but must remain guarded from differentiation and senescence. Here we show that Cbx4, a Polycomb Repressive Complex-1 (PRC1)-associated protein, maintains human epidermal stem cells slow-cycling and undifferentiated, while protecting them from senescence. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10332

8 Samples

Download data: TXT

(Submitter supplied) Human epidermal stem cells transit from a slow cycling to an actively proliferating state to contribute to homeostasis. Both stem cell states differ in their cell cycle profiles but must remain guarded from differentiation and senescence. Here we show that Cbx4, a Polycomb Repressive Complex-1 (PRC1)-associated protein, maintains human epidermal stem cells slow-cycling and undifferentiated, while protecting them from senescence. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

19 Samples

Download data: TXT

(Submitter supplied) To gain unbiased insight into the association of NIPP1 with regulatory, coding and intergenic regions of the human genome, DamID experiments and subsequent analysis by ENCODE arrays were performed. The DamID method uses fusions of the bacterial Dam DNA methylase and the protein of interest, to direct the enzymatic activity to the protein’s genomic binding sites, where the DNA is methylated. Methylated DNA is then extracted, enriched and further analysed by microarray. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6129

2 Samples

Download data: BAR, BED, CEL

(Submitter supplied) NIPP1, an established interactor of protein phosphatase 1 (PP1), is implicated in PRC2-mediated regulation of gene expression. Here, we explore whether PP1 associated with NIPP1 is involved in NIPP1-mediated regulation of genes. Therefore, we generated Hela Tet-off (HTO) cell lines that stably and inducibly express a Flag-tagged version of wild-type NIPP1 (HTO-NIPP1wt) or mutant NIPP1 (HTO_NIPP1m). The latter mutant lacks the major PP1 binding site by two point mutations in the RVXF-motif, an established PP1 - binding motif. All cell lines were derived from the same parental HeLa Tet-Off (HTO-PT) cell line which expresses only tTA transactivator and is used as a control. The Flag fusions were only expressed in the absence of doxycyline and at levels that were up to twofold higher than that of endogenous NIPP1. We performed a gene expression profiling of the HTO cell lines, using Whole Human Genome Oligo microarrays from Agilent. A Paired SAM analysis identified 1365 genes with an altered expression (P < 0.01) between the Flag-NIPP1 and parental cell lines. Importantly, only 185 genes were differentially expressed (P<0.01) between the Flag-NIPP1m and parental cell lines. Even more strikingly, only 5% of the genes that were affected by the expression of Flag-NIPP1 also showed a significantly different expression in the Flag-NIPP1m cells. A similar small overlap was noted when the analysis was restricted to the 50 genes that were most upregulated or downregulated by the expression of Flag-NIPP1. Finally, scatter plot analysis revealed no significant correlation between the genes that were affected by the expression of Flag-NIPP1 or Flag-NIPP1m. Collectively, these data demonstrate that a moderate increase in the concentration of NIPP1 affects the expression of numerous genes by a mechanism that depends on associated PP1.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

12 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9185 GPL1261

4 Samples

Download data: BED, CEL, CHP, TXT