GEO DataSets

(Submitter supplied) Investigation of whole genome gene expression level changes in HCT116 cells upon knockdown of Tip60 or p400, compared to control siRNA-transfected cells. Two different siRNA directed against Tip60 were used and experiments were done in duplicate. Same for p400-targetting or control siRNA.

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL10191

12 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15975 GPL10191

14 Samples

Download data: PAIR

(Submitter supplied) The chromatin remodeller p400 has oncogenic properties that promote early steps of colon cancer. Chromatin immunoprecipitation (ChIP) of p400 together with chromatin profiling by ChIP-on-chip analysis demonstrated that p400 directly binds the chromatin at promoters of p400 target genes.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15975

2 Samples

Download data: PAIR

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL6771 GPL6770 GPL4134

14 Samples

Download data: TXT

(Submitter supplied) Proper regulation of chromatin structure is necessary for the maintenance of cell type-specific gene expression patterns. The embryonic stem cell (ESC) expression pattern governs self-renewal and pluripotency. Here, we present an RNAi screen in mouse ESCs of 1008 loci encoding chromatin proteins. We identified 68 proteins that exhibit diverse phenotypes upon knockdown (KD), including seven subunits of the Tip60-p400 complex. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6770 GPL6771

2 Samples

Download data: TXT

(Submitter supplied) Proper regulation of chromatin structure is necessary for the maintenance of cell type-specific gene expression patterns. The embryonic stem cell (ESC) expression pattern governs self-renewal and pluripotency. Here, we present an RNAi screen in mouse ESCs of 1008 loci encoding chromatin proteins. We identified 68 proteins that exhibit diverse phenotypes upon knockdown (KD), including seven subunits of the Tip60-p400 complex. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

12 Samples

Download data: TXT

(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

39 Samples

Download data: BEDGRAPH

(Submitter supplied) Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

16 Samples

Download data: XLSX

(Submitter supplied) Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: BEDGRAPH

(Submitter supplied) Previous studies in our laboratory have shown that low folate diet (control diet with 2mg folate/kg, low folate diet with 0.3mg folate/kg) can induce intestinal tumors in BALB/c mice. We used microarrays to compare MTHFR+/+ BALB/c mice fed control diet and MTHFR+/- BALB/c mice fed low folate diet.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5377

Platform:

GPL6246

8 Samples

Download data: CEL

Analysis of intestine from MTHFR+/- BALB/c mice fed a low folate diet (0.3mg/kg) for 1 yr. The MTHFR C677T polymorphism is associated with risk for colorectal cancer. Results provide insight into mechanisms underlying the impact of folate and MTHFR deficiency on tumorigenesis.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 2 protocol sets

Platform:

GPL6246

Series:

GSE34011

8 Samples

Download data: CEL

(Submitter supplied) The goal was to investigate genome-wide if JAZF1 influences the deposition as well as the acetylation of the histone variant H2A.Z. ChIP-seq analysis revealed that depletion of JAZF1 leads to reduced acetylation of H2A.Z at specific sites.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: BW

(Submitter supplied) The goal was the investigation of JAZF1's possible role in regulating gene expression. RNA-seq analysis revealed that depletion of JAZF1 results in transcriptome changes that affect, among others, ribosome biogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

10 Samples

Download data: CSV

(Submitter supplied) Ankrd11 is a potential chromatin regulator implicated in neural development and autism spectrum disorder (ASD) with no known function in the brain. Here, we show that knockdown of Ankrd11 in developing murine or human cortical neural precursors caused decreased proliferation, reduced neurogenesis, and aberrant neuronal positioning. Similar cellular phenotypes and aberrant ASD-like behaviors were observed in Yoda mice carrying a point mutation in the Ankrd11 HDAC-binding domain. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

11 Samples

Download data: CEL

(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 array

Platforms:

GPL13112 GPL10333

15 Samples

Download data: TXT

(Submitter supplied) The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: TXT

(Submitter supplied) To identify the functional role of Hdac6 in embryonic stem cells, we examined gene expression changes in mouse ES cells upon Tip60, Hdac6 and double knockdown.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

8 Samples

Download data: TXT

(Submitter supplied) EPC1/TIP60-mediated histone acetylation facilitates spermiogenesis in mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15103

2 Samples

Download data: TXT