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Links from GEO DataSets

Items: 20

1.

Transcriptome analysis and Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing

(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
Series
Accession:
GSE66167
ID:
200066167
2.

Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing (RRBS)

(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
Series
Accession:
GSE66121
ID:
200066121
3.

Transcriptome analysis in chronic lymphocytic leukemia cells using RNA sequencing (RNA-seq)

(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
4.

Epigenetic regulation of miRNA in CLL [MCIp_hsa_miRNA_v3b]

(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
Series
Accession:
GSE33623
ID:
200033623
5.

Epigenetic regulation of miRNA in CLL

(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
Series
Accession:
GSE33347
ID:
200033347
6.

Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v3b]

(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
Series
Accession:
GSE33305
ID:
200033305
7.

Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v2]

(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
Series
Accession:
GSE33304
ID:
200033304
8.

Epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking

(Submitter supplied) Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called super-enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the enhancers of the immunoglobulin heavy chain locus (IGH) and proto-oncogene CCND1 that are common in B-cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterised the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL20301
16 Samples
Download data: BED, BROADPEAK, BW, NARROWPEAK
Series
Accession:
GSE151556
ID:
200151556
9.

Genome wide DNA methylation in oral squamous cell carcinoma (OSCC) disease and adjacent normal tissue samples

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
21 Samples
Download data: IDAT
Series
Accession:
GSE87053
ID:
200087053
10.

Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia

(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
Series
Accession:
GSE32698
ID:
200032698
11.

Gene expression and methylation profiling of IGHV Unmutated vs mutated CLL

(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:
GPL16699 GPL10878
40 Samples
Download data: TXT
Series
Accession:
GSE81937
ID:
200081937
12.

Methylation Profiling of IGHV Unmutated vs mutated CLL

(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
Series
Accession:
GSE81936
ID:
200081936
13.

Gene Expression profiling in IGHV Unmutated vs mutated CLL

(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
Series
Accession:
GSE81935
ID:
200081935
14.

MeDIP-chip result of 10 lung cancer patients

(Submitter supplied) Compared with non-cancerous lung tissues, lung cancer in Xuanwei tissues expressed a total of 6,899 differentially methylated regions, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Many differentially methylated regions have been found in lung cancer in Xuanwei.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL16378
2 Samples
Download data: GFF, PAIR, XLS
Series
Accession:
GSE113432
ID:
200113432
15.

The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes

(Submitter supplied) Background: C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: XLSX
Series
Accession:
GSE111420
ID:
200111420
16.

Gene expression profiling in liver normal and tumor tissues in C3H mice

(Submitter supplied) We have employed microarray analysis to detect tumor-related genes of liver tissues in C3H mice
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL13912
6 Samples
Download data: TXT
Series
Accession:
GSE104627
ID:
200104627
17.

Gene expression profiling in Hepa1c1c7 transfected Mst1r or Slpi

(Submitter supplied) To analysis Mst1r and slpi function as a tumor associated gene, we carried out overexpression analysis of Mst1r or Slpi to Hepa1c1c7 and investigated downstream genes expression by microarray.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL21163
3 Samples
Download data: TXT
Series
Accession:
GSE104626
ID:
200104626
18.

Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer's disease

(Submitter supplied) Recent work has identified roles for environmental, genetic and epigenetic factors in AD risk. Motivated by suspected roles for epigenetic modifications in AD, we performed a genome-wide screen of DNA methylation using the Illumina Infinium HumanMethylation450 array platform on bulk tissue samples from the superior temporal gyrus (STG) of AD cases and non-demented controls. We paired a sliding window approach with linear models that account for age, gender, ethnicity, and estimated cellular proportions (neuronal vs. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
68 Samples
Download data: TXT
Series
Accession:
GSE76105
ID:
200076105
19.

HM450K-based DNA methylation analysis of normal and Chronic Phase-Chronic Myeloid Leukemia (CP-CML)

(Submitter supplied) We analysed genome wide DNA methylation of mature (CD34-CD15+) and immature (CD34+CD15-) hematopoietic cells from patients with chronic phase CML at diagnosis. before any treatment. and compared it to their counterpart cells isolated from healthy donors.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
23 Samples
Download data: IDAT, TXT
Series
Accession:
GSE106600
ID:
200106600
20.

Multi-omics analysis reveals divergent epigenetic regulation of gene expression and drivers of esophageal squamous cell carcinoma [ChIP-seq]

(Submitter supplied) Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
2 Samples
Download data: BED
Series
Accession:
GSE151838
ID:
200151838
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