GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL10999

12 Samples

Download data: BW

(Submitter supplied) Mapping the locations of the DNA binding protein CTCF genome-wide to assess its colocalisation with expression domain boundaries.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BW

(Submitter supplied) The histone modification H3K27me3 is representative of silenced regions of the genome. Changes between the normal and cancer state were investigated.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: BW

(Submitter supplied) H3K4me3 ChIP-seq was done to examine transcription start sites in a genome wide manner, and compare results to CAGE-seq

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BW

(Submitter supplied) DNA methylation was measured by MBD2 enrichment of DNA fragments in IMR90. A statistical model was developed to estimate absolute methylation levels, and compared to whole genome bisulfite sequencing results (Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature)

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: BW

(Submitter supplied) Capped analysis of gene expression (CAGE) sequencing was done on a normal and a cancer cell line to examine how promoter usage changes between these two states.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: BW

(Submitter supplied) Strand-specific RNA sequencing was done on a normal and a cancer cell line to examine how isoforms are used differently between these two states.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: BW

(Submitter supplied) To investiagate copy number differences between PrEC and LNCaP cells, each was DNA sequenced.

Organism:

Homo sapiens

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL10999

2 Samples

Download data: BW

(Submitter supplied) To screen for epigenetically silenced miRNAs, wecarried out miRNA microarray analysis in three colorectal cancer (CRC) cell lines (HCT116, DLD-1 and RKO) treated with or without 5-aza-2'-deoxycytidine (aza). HCT116 and RKO cells were also treated with aza plus 4-phenylbutyric acid (PBA). In addition, we analyzed HCT116 cells in which the DNA methyltransferase genes DNMT1 and DNMT3B were genetically disrupted (double knockout; DKO cells), thereby abrogating DNA methylation. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL6955

10 Samples

Download data: TXT

(Submitter supplied) We identified that miR-1 is silenced in association with CpG island hypermethylation in a colorectal cancer (CRC) cell line, HCT116. To determine whether miR-1 serves as a tumor suppressor in CRC, we transfected CRC cell lines with a miR-1 precursor molecule or a negative control, and carried then out a series of MTT assays. Forty-eight hours after transfection, we observed that ectopic expression of miR-1 moderately suppressed growth in all three cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL5082 GPL6244

14 Samples

Download data: BAR, CEL

(Submitter supplied) To identify genomic regions which display concordant gene expression in prostate cancer, we performed expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP. These expression arrays were integrated ChIP-on-chip studies of active and repressive epigenetic marks in same cells to discover and characterise regions of Long Range Epigenetic Silencing (LRES) in prostate cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

4 Samples

Download data: CEL

(Submitter supplied) To identify genomic regions which display concordant epigenetics alterations in prostate cancer, we performed MeDIP and ChIP-on-chip profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP. These promoter arrays were integrated with expression arrays of the same cells to discover and characterise regions of Long Range Epigenetic Silencing (LRES) in prostate cancer.

Organism:

Homo sapiens

Type:

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

Platform:

GPL5082

10 Samples

Download data: BAR, CEL

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL9998

7 Samples

Download data: TXT

(Submitter supplied) We found frequent epigenetic silencing of microRNA-34b/c in human colorectal cancer. Introduction of miR-34b/c into a colorectal cancer cell line induced significant changes in gene expression profile. We also found overlap between the genes downregulated by miR-34b/c and those downregulated by DAC. Keywords: dose response

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

5 Samples

Download data: TXT

(Submitter supplied) aCGH was used to profile copy-number aberrations (CNA) in 64 glioblastoma specimen of patients treated within clinical trials. The data was used to identify changes in CNA which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4421

64 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

77 Samples

Download data: IDAT

(Submitter supplied) H2A.Z is an evolutionarily conserved H2A variant implicated in the regulation of gene expression, however its role in transcriptional deregulation in cancer remains poorly understood. Using genome-wide studies, we investigated the role of promoter-associated H2A.Z and acetylated H2A.Z (acH2A.Z) in gene deregulation and its relationship with DNA methylation and H3K27me3 in prostate cancer. Our results reconcile the conflicting reports of positive and negative roles for histone H2A.Z and gene expression states. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5082

8 Samples

Download data: BAR, CEL

(Submitter supplied) Abstract: DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate DNA methylation status of CpG sites in a targeted or genome-wide fashion but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing; Genome variation profiling by SNP array

Platforms:

GPL6801 GPL9115 GPL5082

40 Samples

Download data: CEL, MAP, TXT

(Submitter supplied) The primary goal of this study was to assess differences in gene expression between prostate cancer cell lines and normal prostate epithelial and stromal cells in primary culture.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

9 Samples

Download data: CEL, CHP