Similar studies for GEO DataSets (Select 200160645) - GEO DataSets

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Items: 20

Select item 2001606451.

Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis

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

Organism:: Homo sapiens

Type:: Methylation profiling by array; Expression profiling by array

Platforms:: GPL23126 GPL13534
31 Samples

Download data: CEL, IDAT

Series

Accession:: GSE160645

ID:: 200160645

Select item 2001568772.

Gene expression data from formalin-fixed paraffin-embedded (FFPE) human uveal melanoma tumors; subset early metastasis vs subset no metastasis

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation correlated to gene expression in relation to survival data.We sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL23126
8 Samples

Download data: CEL

Series

Accession:: GSE156877

ID:: 200156877

Select item 2001568763.

llumina 450k array was used to identify DNA methylation data from formalin-fixed paraffine-embedded (FFPE) human uveal melanoma correlated to gene expression, metastasis and poor prognosis

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation in relation to histopathological classification and survival data. In addition, we sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
23 Samples

Download data: IDAT, TXT

Series

Accession:: GSE156876

ID:: 200156876

Select item 2000665554.

Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays (HM 450K).

(Submitter supplied) Comparative analysis of reproducibility of Fresh Frozen (FF) derived DNA, FFPE derived DNA and FFPE derived DNA restored using the Infinium FFPE DNA Restoration solution (FFPEr) when used on the Infinium HumanMethylation450 BeadChip assay.

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
65 Samples

Download data: TXT

Series

Accession:: GSE66555

ID:: 200066555

Select item 2001134325.

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

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001303576.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array

Platforms:: GPL21145 GPL13534 GPL18573
26 Samples

Download data: IDAT, TAB

Series

Accession:: GSE130357

ID:: 200130357

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001303567.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [RNA-Seq]

(Submitter supplied) The strong association between BAP1 mutations and highly aggressive Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression. Thus, we characterized the impact of BAP1 loss on the DNA methylome in UM.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
6 Samples

Download data: TAB

Series

Accession:: GSE130356

ID:: 200130356

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2001303548.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [BeadChip 450K]

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
12 Samples

Download data: IDAT, TXT

Series

Accession:: GSE130354

ID:: 200130354

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001302959.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [MethylationEPIC]

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
8 Samples

Download data: IDAT, TXT

Series

Accession:: GSE130295

ID:: 200130295

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002338610.

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

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

Organism:: Homo sapiens

Type:: Expression profiling by array

Platforms:: GPL8432 GPL6883
50 Samples

Download data

Series

Accession:: GSE23386

ID:: 200023386

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002338511.

Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples)

(Submitter supplied) The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6883
25 Samples

Download data: TXT

Series

Accession:: GSE23385

ID:: 200023385

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002338412.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL8432
25 Samples

Download data: TXT

Series

Accession:: GSE23384

ID:: 200023384

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20012936413.

Genome-wide DNA methylation analysis of colorectal adenomas with and without recurrence reveals an association between CpG methylation and histological subtypes.

(Submitter supplied) Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development and may also lead to colorectal cancer (CRC) formation. While gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and non-recurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set (n=72) of formalin-fixed paraffin-embedded (FFPE) primary colorectal adenomas without recurrence (n=30), primary adenomas with recurrence at the same location (n=19), so-called “matched pair samples” (n=10; comprising the primary adenoma and the recurrent adenoma) and normal mucosa specimens (n=3). more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
72 Samples

Download data: IDAT, TXT

Series

Accession:: GSE129364

ID:: 200129364

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003318114.

Feasibility and Interpretation of the Genome-wide Infinium Methylation Data Derived from Ligated Formalin Fixed Paraffin Embedded Paired Tumor and Normal Tissue.

(Submitter supplied) Formalin-fixed paraffin-embedded (FFPE) samples are a highly desirable resource for epigenetic studies, but there is no suitable platform to assay genome-wide methylation in these widely available resources. Recently, Thirwell et al. (2010) have reported a modified ligation-based DNA repair protocol to prepare FFPE DNA for the Infinium methylation assay. In this study, we have tested the accuracy of methylation data obtained with this modification by comparing paired fresh-frozen (FF) and FFPE colon tissue from colorectal cancer patients. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
48 Samples

Download data: TXT

Series

Accession:: GSE33181

ID:: 200033181

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009258015.

Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours

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

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platforms:: GPL21145 GPL13534
37 Samples

Download data: IDAT

Series

Accession:: GSE92580

ID:: 200092580

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009257916.

Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (EPIC)

(Submitter supplied) DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL21145
25 Samples

Download data: IDAT

Series

Accession:: GSE92579

ID:: 200092579

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009257717.

Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (450K)

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL13534
12 Samples

Download data: IDAT

Series

Accession:: GSE92577

ID:: 200092577

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004099018.

Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

(Submitter supplied) For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL13912
28 Samples

Download data: TXT

Series

Accession:: GSE40990

ID:: 200040990

Select item 20002213819.

Expression Data from Uveal Melanoma primary tumors.

(Submitter supplied) A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors. Metastasis free survival analysis was performed to obtain clinical and genomic variables associated to metastasis occurrence. more...