Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EMT

ABSTRACT: three pairs of isogenic human mammary epithelial and fibroblast cells, were used to characterized cell type specific dna methylation using using methyla cytosin immunoprecipitation

ORGANISM(S): Homo sapiens

SUBMITTER: Petr Novak

PROVIDER: E-MEXP-3651 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cell-type specific DNA methylation patterns define human breast cellular identity.

Novak Petr P Stampfer Martha R MR Munoz-Rodriguez Jose L JL Garbe James C JC Ehrich Mathias M Futscher Bernard W BW Jensen Taylor J TJ

PloS one 20121220 12

DNA methylation plays a role in a variety of biological processes including embryonic development, imprinting, X-chromosome inactivation, and stem cell differentiation. Tissue specific differential methylation has also been well characterized. We sought to extend these studies to create a map of differential DNA methylation between different cell types derived from a single tissue. Using three pairs of isogenic human mammary epithelial and fibroblast cells, promoter region DNA methylation was ch ...[more]

PMID: 23284978

Similar Datasets

DNA methylation of miRNA genes in HMEC and HMF

Project description:Normal cell type specific DNA methylation of miRNA genes. HMEC and HMF represent two distinct differentiated cell type present in mammary gland each with a distinct phenotype, a distinct epigenotype as well as distinct miRNA expression pattern. The aim of the study was to determine how epigenetic modifications including DNA methylation effect miRNA expression. Two cell types HMEC vs. HMF. Biological replicates: 3 pairs of HMEC-HMF of 3 distinct genotypes. Immunoprecipitation using anti-Methylcytosine (5MeC) antibody.

2011-04-05 | E-GEOD-28374 | biostudies-arrayexpress

Aberrant DNA methylation of miRNA genes in breast cancer

Project description:Aberrant DNA methylation is frequently observed in cancer. The aim of the study was to determine how is DNA methylation of miRNA genes changed in breast cancer cell lines an breast tumor specimens. Breast cancer cell lines vs. HMEC. Breast tumor tissue specimens vs. non-tumor tissue specimens. Biological replicates: 12 breast tumor specimens, 5 breast non-tumor specimens, 7 breast cancer cell lines, 3 HMEC genotypes, 3 HMF genotypes. Immunoprecipitation using anti-Methylcytosine (5MeC) antibody.

2012-05-25 | E-GEOD-38254 | biostudies-arrayexpress

miRNA genes in HMEC and HMF

Project description:This SuperSeries is composed of the following subset Series: GSE28374: DNA methylation of miRNA genes in HMEC and HMF GSE28375: Histone H3 acetylation of miRNA genes in HMEC and HMF GSE28376: Histone H3 lysine 27 trimethylation of miRNA genes in HMEC and HMF GSE28377: Histone H3 lysine 4 trimethylation of miRNA genes in HMEC and HMF GSE28378: Histone H3 lysine 9 dimethylation of miRNA genes in HMEC and HMF Refer to individual Series

2011-04-05 | E-GEOD-28380 | biostudies-arrayexpress

DNA methylation of mortal and immortal breast cells

Project description:DNA methylation changes during immortalization of breast cells. The aim of the study was to determine whether differential epigentic state of TERT gene is involved in immortalization of breast cells. comparison of Pre-Stasis, Post-Selection, and immortal cells

2013-07-03 | E-GEOD-48447 | biostudies-arrayexpress

Methylation profiling of different stages of human mammary epithelial cells from pre-statis to cancer

Project description:To characterize early epigenetic events in breast carcinogenesis, we analyzed DNA methylation state of different stages of HMECs from pre-stasis to cancer cell lines using human promoter microarray

2009-01-01 | E-MEXP-1889 | biostudies-arrayexpress

Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (miRNA dataset)

Project description:Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after arsenic-induced malignant transformation. Arsenite-transformed RWPE-1 cells (n=2) are compared to parental RWPE-1 cells (n=2). Normal PrEC (n=2) are included for comparison. Immunoprecipitation using anti-methylcytosine (5MeC) antibody.

2012-06-25 | E-GEOD-38929 | biostudies-arrayexpress

Efficient immortalization of normal human mammary epithelial cells using two pathologically relevant agents does not require gross genomic alterations

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

2013-07-03 | E-GEOD-48504 | biostudies-arrayexpress

Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 1)

Project description:Aberrant DNA methylation is frequently observed in cancer. The aim of this study was to determine how DNA methylation is changed after toxicant-induced malignant transformation. This study also puts the DNA methylation changes into context with respect to the aberrant DNA methylation events that occur in bladder and prostate carcinogenesis not associated with toxicant exposure. Immortalized UROtsa (n=3) and RWPE-1 (n=2) are compared to normal HUC (n=2) and PrEC (n=2), respectively. Arsenite (n=1), monomethylarsonous acid (n=2) or cadmium (n=1) transformed UROtsa are compared to parental UROtsa (n=3). Arsenite (n=2), cadmium (n=1) or MNU (n=1) transformed RWPE-1 cells are compared to parental RWPE-1 cells (n=2). Clinical bladder tumor biopsies (n=6), urothelial carcinoma cell lines (n=2) and prostate cancer cell lines (n=3) are compared to thier normal tissue counterparts HUC (n=2) and PrEC (n=2). Immunoprecipitation using anti-methylcytosine (5MeC) antibody.

2012-06-25 | E-GEOD-38926 | biostudies-arrayexpress

Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 2)

2012-06-25 | E-GEOD-38928 | biostudies-arrayexpress

Comparative genomic hybridization of human breast carcinomas

Project description:Roswell Park Human 19K Array CGH the format of the data is: Reporter Identifier Band Count - number of replicate spots the data represents (some spots are excluded in image analysis, usually because they are too dim to be reliable) chr - Chromosome Start - Start location in base pairs Stop - Stop Location in Base pairs Center - Center in base pairs g_loc - graphing location this is the location of the center in base pairs if the chromosomes were laid end to end Log2 ratio - log2 ratio (test/control) Ratio - linear version of the ratio above A - Measure of brightness A=(log2 cy3 + log2 cy5)/2 Flag - Used to color code spots 3 - red probably mismapped 4 - green potentially polymorphic 5 - light blue Shows a high degree of duplication with other area in the genome (see UCSC genome browser) reference - Reference for why the clone was flagged Pub Med link - Pub Med ID for why clone was flagged

2009-06-01 | E-MEXP-2141 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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