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Links from GEO DataSets

Items: 20

1.

Gene expression profiling of Acute Myeloid Leukemia (AML) samples

(Submitter supplied) The aim was to analyze the expression of genes in cytogenetically distinct cases of AML.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL9851
6 Samples
Download data
Series
Accession:
GSE34722
ID:
200034722
2.

Genome-Wide Analysis of Acute Myeloid Leukemia Reveals Leukemia-Specific Methylome and Subtype-Specific Hypomethylation of Repeats

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL9115 GPL9851
22 Samples
Download data: GFF, WIG
Series
Accession:
GSE37022
ID:
200037022
3.

Genome-wide study of DNA methylation in AML by MeDIP-seq

(Submitter supplied) Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML) we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9115
16 Samples
Download data: GFF, TXT, WIG
Series
Accession:
GSE28314
ID:
200028314
4.

methylatedDNA_peripheralBlood

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
4 related Platforms
4 Samples
Download data
Series
Accession:
GSE8810
ID:
200008810
5.

Methylation profiling of leukemia cell lines

(Submitter supplied) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. We developed a novel and robust technique that allows the unbiased, genome wide detection of CpG-methylation in limited DNA samples, without applying methylation-sensitive restriction endonucleases or bisulfite-treatment. The approach is based on a recombinant, methyl-CpG binding protein that efficiently binds CpG-methylated DNA depending on its degree of CpG methylation. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL2040
10 Samples
Download data
Series
Accession:
GSE4009
ID:
200004009
6.

Expression profiling of leukemia cell lines

(Submitter supplied) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. Genome wide methylation profiling of myeloid leukemia cell lines identified a large number of genes with aberrantly methylated CpG islands. Comparative mRNA expression analysis suggests that more than half of these genes show extremely low or absent expression in normal cells, suggesting that hypermethylation in cancer may be independent of the transcriptional status of the affected gene. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by array
Dataset:
GDS2251
Platform:
GPL570
4 Samples
Download data
Series
Accession:
GSE3280
ID:
200003280
7.
Full record GDS2251

Myeloid leukemia cell lines

Comparison of myeloid leukemia cells to normal monocytes. Transcriptional status of each gene compared to its CpG methylation state. The methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor suppressor genes.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 4 cell line, 2 disease state sets
Platform:
GPL570
Series:
GSE3280
4 Samples
Download data
DataSet
Accession:
GDS2251
ID:
2251
8.

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(Submitter supplied) Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9052
3 Samples
Download data: BAM, GFF
Series
Accession:
GSE21714
ID:
200021714
9.

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia

(Submitter supplied) Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL10999 GPL11154
19 Samples
Download data: TXT
Series
Accession:
GSE37454
ID:
200037454
10.

Comparative DNA methylome analysis of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium

(Submitter supplied) Classically, there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I; and uterine papillary serous carcinoma (UPSC), or Type II. These two types of cancers exhibit distinct DNA methylation levels in promoters of many genes. In EAC, many tumor suppressor genes were silenced due to DNA hypermethylation at their promoter region. However, promoters of many of these genes remained unmethylated in UPSC. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL11154 GPL10999
14 Samples
Download data: BW
Series
Accession:
GSE51565
ID:
200051565
11.

Whole-genome DNA methylation profiling of 152 pediatric AML patients

(Submitter supplied) Genome-wide CpG-island methylation profiling on pediatric AML samples was performed to identify specific methylation patterns discriminating particular AML subgroups from the rest of AML samples based on the methylation profile.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL9767
152 Samples
Download data: TXT
Series
Accession:
GSE100284
ID:
200100284
12.

Genome-Wide Screen of Promoter Methylation Identifies Novel Markers for Tumor Development in Melanoma

(Submitter supplied) Background: DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. In particular, dysregulation of promoter methylation in cancer has already been shown to be associated with repression of tumor suppressors and activation of oncogenes. In addition, detection of altered promoter methylation status is suitable for the design of diagnostic or prognostic tests. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL6484 GPL6602
43 Samples
Download data: PAIR
Series
Accession:
GSE13706
ID:
200013706
13.

Global DNA methylation study of trisomy 8 AML

(Submitter supplied) We report the application of methylated DNA immunoprecipitation followed by next-generation sequencing to trisomy 8 AML. Through a global study and quantifying the methylation signals, we demonstrated a characteristic DNA methylation distribution for trisomy 8 indicating the impact of the hypermethylation of the extrachromosome 8 on suppressing the signals on the rest of the chromosomes.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL10999
3 Samples
Download data: GFF, WIG
Series
Accession:
GSE38483
ID:
200038483
14.

Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq).

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...
Organism:
Gallus gallus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9385
2 Samples
Download data: TXT
Series
Accession:
GSE56975
ID:
200056975
15.

Genome-wide DNA methylation analysis of breast cancer

(Submitter supplied) Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
188 Samples
Download data: TXT
Series
Accession:
GSE75067
ID:
200075067
16.

Genome-wide DNA methylation analysis of different cell types

(Submitter supplied) We performed whole-genome methylation analysis using 450K Illumina BeadArrays on different human cell types. In total 24 experiments were performed. Dermal fibroblasts, three different epidermal melanocytes (dark, medium and light pigmentation), epidermal keratinocytes, mammary fibroblasts, mammary epithelial cells, mammary endothelial cells and mesenchymal stem cells were analyzed in technical duplicates. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
24 Samples
Download data: IDAT, TXT
Series
Accession:
GSE74877
ID:
200074877
17.

DNA Methylation Identifies Epigenetic Variation across Embryo and Endosperm in Maize (Zea may)

(Submitter supplied) Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues.
Organism:
Zea mays
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL15463
2 Samples
Download data: BED
Series
Accession:
GSE58549
ID:
200058549
18.

Acute myeloid leukemia study

(Submitter supplied) Acute myeloid leukemia study. Supplementary Table 1: Clinical, morphological, cytogenetic and molecular genetic information on 116 AML patient samples. Supplementary Table 2: Summary of the distribution of clinical and molecular genetic characteristics within the AML sample set. Supplementary Table 3: Fluorescence ratios of the 6,283 well-measured and variably-expressed genes. Supplementary Table 4: Clinical and laboratory characteristics of normal karyotype predominant subtypes I and II. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Datasets:
GDS841 GDS843
Platforms:
GPL318 GPL319 GPL317
119 Samples
Download data
Series
Accession:
GSE425
ID:
200000425
19.
Full record GDS843

Adult acute myeloid leukemia: bone marrow and peripheral blood expression profiles (SHDJ)

Part of a study profiling 54 bone marrow and 65 peripheral blood samples from 116 adults with acute myeloid leukemia (AML). Results identify distinct gene expression signatures that correlate with clinical outcomes. Signatures used to construct a clinical outcome predictor using 133 genes.
Organism:
Homo sapiens
Type:
Expression profiling by array, log ratio, 3 disease state, 2 genotype/variation, 2 tissue sets
Platform:
GPL319
Series:
GSE425
49 Samples
Download data
DataSet
Accession:
GDS843
ID:
843
20.
Full record GDS841

Adult acute myeloid leukemia: bone marrow and peripheral blood expression profiles (SHCO)

Part of a study profiling 54 bone marrow and 65 peripheral blood samples from 116 adults with acute myeloid leukemia (AML). Results identify distinct gene expression signatures that correlate with clinical outcomes. Signatures used to construct a clinical outcome predictor using 133 genes.
Organism:
Homo sapiens
Type:
Expression profiling by array, log ratio, 2 disease state, 2 genotype/variation, 2 tissue sets
Platform:
GPL317
Series:
GSE425
26 Samples
Download data
DataSet
Accession:
GDS841
ID:
841
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