Genome-wide methylation and expression analysis of two breast cancer cell lines
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ABSTRACT:
PROVIDER: PRJNA193491 | ENA |
REPOSITORIES: ENA
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Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). DNA Methylation was assayed for two breast cancer cell lines using Methyl-MAPS.
2013-06-15 | E-GEOD-45336 | biostudies-arrayexpress
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research).
2013-06-15 | GSE45336 | GEO
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research).
2013-06-15 | GSE45335 | GEO
Project description:To evaluate the methylation profiles of breast cell lines, we performed methylation profiling of 55 well-characterized breast cancer cell lines on the Illumina HumanMethylation27 (HM27) platform and made use of publicly available methylation profiles of primary breast tumors for comparison. The available annotation for each cell line includes estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status, as well as the tumor type, and the age of each patient. Additionally, recent publications have described genome-wide mRNA expression profiles for most of these lines, and samples were classified on the basis of the expression profile into Basal A (BaA), Basal B/Claudin Low (BaB/CLDNlow) and Luminal (Lu) subtypes. Finally, GI50 has been calculated for these cell lines for 77 approved therapeutic agents. We find that the DNA methylation profiles of breast cancer cell lines largely retain the features that characterize primary tumors, although there are crucial differences as well.
2013-03-01 | GSE42944 | GEO
Project description:To evaluate the methylation profiles of breast cell lines, we performed methylation profiling of 55 well-characterized breast cancer cell lines on the Illumina HumanMethylation27 (HM27) platform and made use of publicly available methylation profiles of primary breast tumors for comparison. The available annotation for each cell line includes estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status, as well as the tumor type, and the age of each patient. Additionally, recent publications have described genome-wide mRNA expression profiles for most of these lines, and samples were classified on the basis of the expression profile into Basal A (BaA), Basal B/Claudin Low (BaB/CLDNlow) and Luminal (Lu) subtypes. Finally, GI50 has been calculated for these cell lines for 77 approved therapeutic agents. We find that the DNA methylation profiles of breast cancer cell lines largely retain the features that characterize primary tumors, although there are crucial differences as well. We assayed DNA methylation in 55 breast cancer cell lines. DNA extracted from breast cell lines was bisulfite treated and hybridized to Illumina HM27 arrays.
2013-03-01 | E-GEOD-42944 | biostudies-arrayexpress
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). RNA-Seq was used to generate mRNA expression profiles of MCF7 and T47D cells under standard growth conditions.
2013-06-15 | E-GEOD-45335 | biostudies-arrayexpress
Project description:Methylation profiling of ten breast cancer cell lines
| PRJEB19340 | ENA
Project description: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). The Cancer Genome Atlas data, incluing methylation profiles of 669 human breast tumors, was utilized for validation. The identified epitypes were characterized by integration with publicly available genome-wide data, including gene expression levels, DNA copy numbers, whole-exome sequencing data, and chromatin states. We identified seven breast cancer epitypes. One epitype was distinctly associated with basal-like tumors and with BRCA1 mutations, one epitype contained a subset of ERBB2-amplified tumors characterized by multiple additional amplifications and the most complex genomes, and one epitype displayed a methylation profile similar to normal epithelial cells. Luminal tumors were stratified into the remaining four epitypes, with differences in promoter hypermethylation, global hypomethylation, proliferative rates and genomic instability. We observed two dominant patterns of aberrant methylation in breast cancer. One pattern, constitutively methylated in both basal-like and luminal breast cancer, was linked to genes with promoters in a Polycomb-repressed state in normal epithelial cells and displayed no correlation to gene expression levels. The second pattern correlated with gene expression levels and was associated with methylation in luminal tumors and genes with active promoters in normal epithelial cells. Our results suggest that hypermethylation patterns in basal-like breast cancer may have limited influence on tumor progression and instead reflects the repressed chromatin state of the tissue of origin. On the contrary, hypermethylation patterns specific to luminal breast cancer influence gene expression, may contribute to tumor progression, and may present an actionable epigenetic alteration in some luminal breast cancers. Genome-wide DNA methylation analysis of 188 breast cancers using Illumina Human Methylation 450K Beadchips.
2016-02-29 | E-GEOD-75067 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and breast cancer samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in breast cancer and normal samples. Samples included 40 normal, 80 breast cancer samples.
2015-03-11 | GSE66695 | GEO
Project description:Genome-wide maps of FLI1 in two GCB cell lines
| PRJNA660420 | ENA