Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA Methylation in Hodgkin's and non-Hodgkin's lymphoma

ABSTRACT: We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. Overall, our study provides a framework for model studies of HL and NHL pathologies. Examination of DNA Methylation in L1236, L428, Reh and Namalwa cell lines.

ORGANISM(S): Homo sapiens

SUBMITTER: Pierre Cauchy

PROVIDER: E-GEOD-51813 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-09-24 | E-GEOD-51814 | biostudies-arrayexpress

Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [Methylation]

Project description:We performed genome-wide DNaseI hypersensitive site in FLT3-ITD and WT patient samples. We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. We examined association patterns of FLT3 ITD and WT AMLs and found that FLT3-ITD signaling is associated with common gene expression and chromatin signature. Examination of DNA methylation patterns in FLT3 ITD and WT AML via microarray study.

2015-07-03 | E-GEOD-64934 | biostudies-arrayexpress

Genome-wide Dnase-Seq profiles in Hodgkin's and non-Hodgkin's lymphoma

Project description:We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. Overall, our study provides a framework for model studies of HL and NHL pathologies. Examination of genome-wide DNaseI hypersensitive sites in L1236, L428, L591, Reh and Namalwa cell lines.

2014-09-24 | E-GEOD-51726 | biostudies-arrayexpress

DNA methylation profiling by array for 67 malignant pleural mesothelioma.

Project description:A Cartes d'Identite des Tumeurs (CIT): Whole-genome DNA methylation was analyzed using the Illumina Infinium HumanMethylation450 Beadchip. Integragen SA (Evry, France) carried out microarray experiments and hybridized to the BeadChip arrays following the manufacturer’s instructions.

2019-03-18 | E-MTAB-6884 | biostudies-arrayexpress

Detection of hypermethylated circulating serum DNA in metastatic breast cancer and confirmation by the cMethDNA assay

Project description:The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR assay for a panel of ten genes, discovered through whole genome methylation array analysis of serum DNA. Cancer-specific methylated DNA was detected in training and test sets of recurrent Stage 4 patient sera with a sensitivity of >90% and a specificity of >96%. A core methylation signature was retained in serum, primary and metastatic tissues throughout the course of the disease, and the cMethDNA assay levels reflected patient response to chemotherapy. Together, our data suggest that the cMethDNA assay can provide a sensitive tool to detect minute levels of tumor DNA present in a vast excess of normal DNA in serum. Samples used: 11 cancer sera,,4 pools of normal leukocytes (5 donors per pool), 6 normal breast tissues microdissected, adjacent to tumor, 15 normal breast tissues, organoid preparations

2014-03-01 | E-GEOD-52621 | biostudies-arrayexpress

Methylation profiling by array of 108 clear cell renal cell carcinoma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French Ligue Nationale Contre le Cancer (<a href=\\ttp://cit.ligue-cancer.net/\\ target=\\_blank\\>http://cit.ligue-cancer.net</a>). Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib.\

2016-02-26 | E-MTAB-3274 | biostudies-arrayexpress

DNA methylome analysis in infants from The Gambia / Aflatoxin / Seasonality study

Project description:Genome wide DNA methylation profiling in infant's blood from a mother/child cohort in The Gambia. The main variables of the analyses were the intra-uterine exposure to aflatoxin B1 (AFB1) and the season of conception. The Illumina Infinium HumanMethylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in whole peripheral blood obtained at 3-6 months of age. A total of 124 samples were analysed, including 3 technical replicates. Bisulphite converted DNA from the 124 samples were hybridised to the Illumina Infinium HumanMethylation 450k Beadchip

2015-04-18 | E-GEOD-59592 | biostudies-arrayexpress

Recurrent TCF12 mutations in anaplastic oligodendroglioma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: Anaplastic oligodendrogliomas (AOs) are rare primary brain tumors which are generally incurable with few treatment targets identified. Most oligodendrogliomas have chromosome 1p/19q co-deletion and IDH mutation. We analyzed 51 AOs by whole-exome and/or transcriptome sequencing identifying previously reported frequent somatic mutations in CIC and FUBP1 genes. We also identified recurrent mutations in TCF12 (11% of IDHmut-codel) which encodes basic helix-loop-helix (bHLFH) transcription factor 12 which is an oligodendrocyte-related transcription factor in IDHmut-codel tumors. Strikingly, the somatic mutations (encoding E548R and R602M substitutions) have not been reported previously in cancer but are identical to germline mutations causing craniosynostosis. Incorporating TCGA data on 43 AO tumors also implicates functional mutation of SMARCA4, NOTCH1, NOTCH2, SETD2, RBPJ and ARID1A/1B. These data are compatible with the combined deregulation of metabolism, chromatin organization/remodeling and Notch-pathway genes in AO oncogenesis. Our analysis provides further insights into the unique and shared pathways driving AO and new targets for therapeutic intervention.

2015-06-15 | E-MTAB-2767 | biostudies-arrayexpress

Differential gene methylation in paired glioblastomas suggests a role of microenvironment in tumor progression

Project description:We sought to analyze DNA methylation levels in paired (initial and recurrence) primary glioblastoma samples to identify candidate pathways that may prone to glioblastoma progression. This study investigates the dynamics of methylation in paired primary GBM.

2015-08-10 | E-MTAB-3476 | biostudies-arrayexpress

Suz12 ChIP-chip using Avi-6k-hu

Project description:The polycomb group (PcG) protein, EZH2, possesses oncogenic properties for which the underlying mechanism is unclear. In this set of experiments, we sought to identify a robust set of Suz12-occupied gene promoters in prostate cancer cell lines. Genome-wide location analysis (ChIP-chip) of SUZ12 was performed in both the PC3 and LNCaP prostate cancer cell lines using an IgG ChIP-chip as a control. There are total 3 hybridizations, including IgG ChIP-chip of PC3 cells, Suz12 ChIP-chip of PC3 and LNCaP cells.

2010-06-25 | E-GEOD-5596 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data