GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL14805 GPL14804

42 Samples

Download data: TXT

(Submitter supplied) Genome-wide profiling of DNA methylation 35 kb upstream and 5 kb downstream of microRNAs in 24 CLL patients and B cells of 2 healthy donors versus a pool of 10 healthy donors.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL14805

26 Samples

Download data: TXT

(Submitter supplied) Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of aberrant epigenetic regulation at the respective regions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14805

11 Samples

Download data: TXT

(Submitter supplied) Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of aberrant epigenetic regulation at the respective regions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL14804

5 Samples

Download data: TXT

(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

Platforms:

GPL10999 GPL11154

111 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

42 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: TXT

(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

Platforms:

GPL10878 GPL16699

40 Samples

Download data: TXT

(Submitter supplied) In the present study, the methylation profiling (MeDIP) was carried out in 14 treatment-naive, early stage (Rai stage 0-2) CLL patients and pooled 19+ normal controls. To find an association of methylation with IGHV mutation status, CLL patients were further segregated into IGHV unmutated (n=9) and IGHV mutated (n=5) subgroups. The methylation signature obtained for CLL versus nornal controls and; unmutated versus mutated CLL was integrated with gene expression profile of these patients and the results were correlated with clinical outcome.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10878

17 Samples

Download data: TXT

(Submitter supplied) In the present study, the gene expression profiling was carried out in 21 early stage CLL patients. A gene expression signature was generated for CLL patients as compared to normal controls; CLL patients were further seggregated into IGHV unmutated (n=10) and IGHV mutated (n=11) subgroups. The expression pattern was confirmed using real time quantitative PCR and the results were correlated with clinical outcome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

23 Samples

Download data: TXT

(Submitter supplied) We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from CLL patient and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated between the two groups. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10999

17 Samples

Download data: BED

(Submitter supplied) Emerging evidences indicate that microRNAs (miRNAs) are often deregulated and have fundamental roles in hepatocellular carcinoma (HCC). However, the mechanism underlying miRNA dysregulation in HCC is still elusive. In this report, we used an integrated analysis strategy combining methylated DNA immunoprecipitation chip (MeDIP-chip) and miRNA expression microarray data to study the correlation between aberrant methylation and dysregulation of miRNA in HCC. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL17532

6 Samples

Download data: PAIR

(Submitter supplied) The goal of this study was to identify genome-wide methylation changes and aberrant gene expression profiles that occur upon deletion of Dnmt3a in a mouse model of CLL and PTCL.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL17021

32 Samples

Download data: TXT

(Submitter supplied) We have analyzed the transcript expression levels in Dicer knock-out embryonic stem (ES) cells 24 hours after transfection with either control siRNA agains Renilla luciferase or miRNA Mimics (Dharmacon) of mmu-miR-290 cluster members in order to identify primary targets of miR-290 cluster miRNAs. Keywords: Comparison of effect of two different transfections on transcriptome of Dicer-KO ES cells

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3430

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) We have analyzed the transcript expression levels in Dicer heterozygous and Dicer knock-out embryonic stem (ES) cells in order to identify which transcripts are regulated by RNAi pathway in mouse ES cells. Keywords: Cell type comparison of cell line with or without knock-out

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3404

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

Analysis of undifferentiated Dicer deficient embryonic stem (ES) cells transfected with the siRNA-like form of miRNAs of the miR-290 cluster. Loss of miRNA pathway components negatively affects ES cell differentiation. Results provide insight into the role of miR-290 in ES cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL1261

Series:

GSE8503

6 Samples

Download data: CEL, CHP

Analysis of embryonic stem (ES) cells homozygous or heterozygous null for Dicer, an RNase III endonuclease required for processing microRNAs. Loss of microRNA pathway components negatively affects ES cell differentiation. Results provide insight into the role of microRNAs in ES cell development.

Organism:

Mus musculus

Type:

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

Platform:

GPL1261

Series:

GSE7141

6 Samples

Download data: CEL, CHP

(Submitter supplied) We report differential DNA methylation results from human femoral atherosclerotic plaques compared to healthy mammary arteries. 5-methylcytosine containing DNA fragments are captured by methylcytosine binding domain - based MethylCapture assay. Captured fragments are sequenced using Illumina paired-end approach and mapped to human genome (hg19). Results. Hypomethylation of chromosomal DNA predominates in atherosclerotic plaques. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: BED