Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Activation of murine CD4+ and CD8+ T lymphocytes leads to dramatic remodeling of N-linked glycans.

doi: 10.4049/jimmunol.177.4.2431

Figure Lengend Snippet: FIGURE 1. Purification of B cells and T cells from mixed splenocytes before and after activation. CD8 T cells, CD4 T cells, and B cells were purified from mixed splenocytes before or after activation using the MACS system with anti-CD8-, anti-CD4-, or anti-CD19-coated magnetic beads, respectively. Phenotypic analysis of purified fresh and activated cell populations was performed by flow cytometry and showed 90% purity of all cell preparations, as indicated. Purified cells were used either for RNA preparation for microarray analysis, or were processed to extract glycans for MALDI profiling and methylation analysis.

Article Snippet: 6 The online version of this article contains supplemental material. at B row n U niversity on M ay 30, 2014 http://w w w .jim m unol.org/ D ow nloaded from Microarray analysis of the expression of cytokine and glycan transferase genes For gene expression analysis, mRNAs were extracted from purified cell populations of fresh and activated lymphocytes and subjected to analysis on a custom Affymetrix-based DNA microarray containing murine and human glycosyltransferase, sulfotransferase, and cytokine genes, made available by the Consortium for Functional Glycomics.

Techniques: Activation Assay, Magnetic Beads, Cytometry, Microarray, Methylation

Journal: Cell

Article Title: DE NOVO EPIGENETIC PROGRAMS INHIBIT PD-1 BLOCKADE-MEDIATED T-CELL REJUVENATION

doi: 10.1016/j.cell.2017.06.007

Figure Lengend Snippet: Key Resources Table

Article Snippet: Taq polymerase–based PCR kit , QIAGEN , Cat#201225.

Techniques: Virus, Recombinant, DNA Methylation Assay, Plasmid Preparation, Cloning, cDNA Synthesis, Microarray, Software, Methylation Sequencing, Flow Cytometry

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: 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