Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Clone Assay, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing

Journal: PLoS ONE

Article Title: DNA Methylation in Multiple Myeloma Is Weakly Associated with Gene Transcription

doi: 10.1371/journal.pone.0052626

Figure Lengend Snippet: (A) Pearson correlation was used to measure linear relationships between DNA methylation and gene expression levels for 1505 CpG probes represented on the GoldenGate Methylation BeadArray. The panels represent examples of a gene with high (left) and low (right) Pearson correlation coefficients when analyzing DNA methylation levels (x axis) against gene expression levels (y axis). (B) A discretization approach was used to classify samples into methylated (M) or unmethylated (U) groups based on the mean ( μ ) methylation value and standard deviation ( σ ) of a given probe. Statistically significant gene expression differences between M and U groups indicated a methylation-expression correlation for the gene in question.

Article Snippet: For these approaches we used DNA methylation data obtained with the GoldenGate BeadArray technology along with corresponding array-based gene expression data from 193 human MM samples.

Techniques: DNA Methylation Assay, Expressing, Methylation, Standard Deviation

Journal: PLoS ONE

Article Title: DNA Methylation in Multiple Myeloma Is Weakly Associated with Gene Transcription

doi: 10.1371/journal.pone.0052626

Figure Lengend Snippet: Box plots represent gene expression levels generated by either microarray or qRT-PCR. Data are shown for samples classified as U or M based on the methylation status of p16 (A), DLC1 (B), IGF1R (C), or IL17RB (D). For microarray data, probe intensities are plotted on the y-axis. Relative fold-change differences are plotted for data generated by qRT-PCR. The number of samples in each group is displayed above each plot. The GoldenGate BeadArray probe names are indicated above each pair of box plots.

Article Snippet: For these approaches we used DNA methylation data obtained with the GoldenGate BeadArray technology along with corresponding array-based gene expression data from 193 human MM samples.

Techniques: Expressing, Generated, Microarray, Quantitative RT-PCR, Methylation