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Methylation profiling of lung squamous cell carcinomas vs surrounding normal tissue

ABSTRACT: Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected. Keywords: Cancer

ORGANISM(S): Homo sapiens

PROVIDER: GSE9622 | GEO | 2007/11/17

SECONDARY ACCESSION(S): PRJNA103473

REPOSITORIES: GEO

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Methylation profiling of lung squamous cell carcinomas vs surrounding normal tissue

Project description:Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected. Keywords: Cancer Comparison of methylation patterns between tumor and matching normal; five patients with stage I lung squamous cell carcinoma

2010-05-25 | E-GEOD-9622 | biostudies-arrayexpress

DNA methylation profiling of ductal carcinoma in situ (DCIS)

Project description:Methylated genomic fragments from tumor DNA and matching normal control were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. MIRA enriched samples from tumor were labeled with Cy5 while MIRA enriched DNA samples from normal tissue were labeled with Cy3. Keywords: Cancer

2009-02-18 | GSE14865 | GEO

DNA methylation profiling of ductal carcinoma in situ (DCIS)

2010-05-05 | E-GEOD-14865 | biostudies-arrayexpress

Analysis of epigenetic changes in human colorectal cancer and matching mucosa tissues

Project description:We used NimbleGen human CpG/promoter microarrays for profiling epigenetic changes (DNA methylation, H3K27me3 and H3K4me3 marks) in colon tumors (Duke's stage II) and matching mucosa samples from patients. Analysis of DNA methylation was done by using the methylated CpG island recovery assay (MIRA) technique with further hybridization versus input on NimbleGen human CpG/promoter microarrays. For profiling of H3K27me3 and H3K4me3 marks, we performed chromatin immunoprecipitation with H3K27me3 (#07-449, Millipore) and H3K4me3 (#39159, Active Motif) antibodies and further hybridized versus input on NimbleGen human CpG/promoter microarrays. All experiments were performed simultaneously for matching tissue samples.

2013-12-31 | E-GEOD-47075 | biostudies-arrayexpress

Comparison of DNA methylation profiles in diploid and transformed tetraploid MEF cells

Project description:We propose that tetraploidy induces epigentic changes including DNA methylation due to the abnormal chromatin in the cells. To test our hypothesis, we employed methylated CpG island recovery assay (MIRA) assisted microarray to determine the DNA methylation profiles in both diploid and tetraploid cells. First, we conducted a methylated-CpG island recovery assay (MIRA). Briefly, we enriched for methylated CpG islands with methylated DNA binding proteins, MBD2/MBD3L1. The pulled down DNA fragments containing CpG islands and input DNA fragments were amplified with real-time PCR. After labeling, they were hybridized to CpG island promoter array. Data were collected and analyzed.

2012-04-29 | E-GEOD-18814 | biostudies-arrayexpress

Autoimunne arthritis-associated B cell methylome in mice with proteoglycan (PG)-induced arthritis (PGIA) [methylation]

Project description:Autoimmune arthritis was induced by three consecutive PG injections. B cells were affinity purified from mice and methylated DNA fractions were enriched by methylated-CpG island recovery assay (MIRA) method and investigated on microarray platforms. Several hundred differentially methylated regions were detected in the investigated B cell epigenomes

2020-05-08 | GSE98939 | GEO

Comparison of DNA methylation profiles in diploid and transformed tetraploid MEF cells

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CpG island hypermethylation in human astrocytomas

Project description:Astrocytomas are common and lethal human brain tumors. Here, we have analyzed the methylation status of over 28,000 CpG islands and 18,000 promoters in normal human brain and in astrocytomas of various grades using the methylated-CpG island recovery assay (MIRA). We identified six to seven thousand methylated CpG islands in normal human brain. ~5% of the promoter-associated CpG islands in normal brain are methylated. Promoter CpG island methylation is inversely and intragenic methylation is directly correlated with gene expression levels in brain tissue. In astrocytomas, several hundred CpG islands undergo specific hypermethylation relative to normal brain with 428 methylation peaks common to more than 25% of the tumors. Genes involved in brain development and neuronal differentiation, such as POU4F3, GDNF, OTX2, NEFM, CNTN4, OTP, SIM1, FYN, EN1, CHAT, GSX2, NKX6-1, RAX, PAX6, DLX2, were strongly enriched among genes frequently methylated in tumors. There was an overrepresentation of homeobox genes and 31% of the most commonly methylated genes represent targets of the Polycomb complex. We identified several chromosomal loci in which many (sometimes more than 20) consecutive CpG islands were hypermethylated in tumors. Seven of such loci were near homeobox genes, including the HOXC and HOXD clusters, and the BARHL2, DLX1, and PITX2 genes. Two other clusters of hypermethylated islands were at sequences of recent gene duplication events. Our analysis offers mechanistic insights into brain neoplasia suggesting that methylation of genes involved in neuronal differentiation, perhaps in cooperation with other oncogenic events, may shift the balance from regulated differentiation towards gliomagenesis. Comparison of methylation patterns of 30 astrocytomas and 6 controls

2010-05-16 | E-GEOD-19391 | biostudies-arrayexpress

CpG island hypermethylation in human astrocytomas

2010-01-01 | GSE19391 | GEO

Methylation profiling of Glioma Stem Cell lines vs GBM FFPE tissue biopsies and foetal Neural Stem Cell lines

Project description:The DNA methylation profiles of Glioma Stem Cell (GSC) lines were investigated in order to find the stem cell signature associated to glioblastoma (GBM). This goal was achieved through the comparison of GSC methylation data with FFPE-GBM biopsies and human foetal Neural Stem Cell (NSC) lines profiles. GSC lines: 3 (GBM2, G144, G166). FFPE-GBM biopsy pool: FFPE-GBM pool: 1 pool from 5 GBM biopsies. Human foetal NSC lines: 2 (CB660 from forebrain; CB660SP form spinal cord). Methylated DNA from each sample was enriched with the immunoprecipitation method using 5-methylcytosine antibody (Eurogentec). Immunoprecipitated DNA (IP-DNA) and total DNA were labeled and hybridized on Agilent Human CpG Island ChIP-on-Chip Microarray 244K. IP-DNA were labeled with Cy5 while the matching total DNA were labeled with Cy3.

2013-03-08 | E-GEOD-41824 | biostudies-arrayexpress

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