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
Project description:Proper DNA-methylation is inevitable for normal development and this epigenetic program is dynamically reprogrammed especially around embryo implantation. Accordingly, embryonic stem cells (ESCs) derived from inner cell mass in pre-implantation embryo exhibit the lowest DNA methylation level compared with differentiated tissue cells to ensure their pluripotency and germ-line potency. Methylated CpG Island Recovery Assay (MIRA) coupled chip DNA methylome analysis demonstrated that Sirt1 deficiency increases the abnormal DNA methylation especially on the a subtype of imprinted and germ-line development genes.
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.
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 Methylation patterns of tumors; six patients with early stage breast cancer (DCIS)
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
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
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.
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
Project description:Elevated DNA methylation in the first intronic region of the BCL6 locus in B cell lymphomas enforces transcription of the BCL6 gene Promoter tiling arrays were used to investigate the distribution of DNA methylation near the promoter region of BCL6 locus Comparison of DNA methylation at promoter regions of lymphoma (Raji) and myeloma (H929) cell lines by methylated CpG island recovery assay (MIRA-chip)
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.
