Biomarker Discovery:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
DNA Methylation Assay:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy
Article Snippet: .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse
Article Snippet: There have been sporadic attempts to apply the human Infinium arrays to primates23–26 and mice.27–29 However, only 1% of Infinium methylation EPIC probes are mappable to the mouse genome, which can lead to array scanning problems, in addition to the cost inefficiency and poor content utilization. .. A custom Infinium array has recently become available targeting 36,000 conserved CpGs in mammals.30 The demand for a DNA methylation microarray is particularly high for the mouse. ..
Microarray:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy
Article Snippet: .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Article Title: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse
Article Snippet: There have been sporadic attempts to apply the human Infinium arrays to primates23–26 and mice.27–29 However, only 1% of Infinium methylation EPIC probes are mappable to the mouse genome, which can lead to array scanning problems, in addition to the cost inefficiency and poor content utilization. .. A custom Infinium array has recently become available targeting 36,000 conserved CpGs in mammals.30 The demand for a DNA methylation microarray is particularly high for the mouse. ..
Functional Assay:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Methylation:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy
Article Snippet: .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy.
Article Snippet: .. To test this, weperformed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNAmethyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, weperformed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNAmethyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
CpG Methylation Assay:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Formalin-fixed Paraffin-Embedded:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Knock-Out:Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNase-H3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. .. Although the reproducibility of the Infinium Mouse Methylation BeadChip is mentioned on the manufacturer site ( https://www.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html ), we have herein confirmed its robustness and reliability using a comprehensive set of different technical, experimental, and biological models.
Article Title: Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.
Article Snippet: .. Description and technical and biological validation of the 285,000 CpG sites mouse DNA methylation microarray. (a) Genomic and functional context of the 280,754 CpG sites contained in the Infinium Mouse Methylation BeadChip microarray: Chromosome location; Infinium design chemistry (Infinium I or II) of the probes; CpG content and neighbourhood context classified in CpG Island, shore, shelf, and other (open sea); functional genomic distribution of the CpG sites classified in gene body, TSS200, TSS1500, and intergenic; distribution among ENCODE candidate cis-Regulatory Elements (cCREs) with promoter-like signature (PLS), with enhancer-like signature (ELS), with distal enhancer location (dELS), with high H3K4me3 and low H3K27ac signal (DNaseH3K4me3), and with CTCF-only elements; and association with an ENCODE representative DNase hypersensitive site (rDHS). (b) Correlation plot of the CpG methylation values to show assay reproducibility of the measurements when using technical replicates on the mouse cell lines C2C12 and HAFTL. (c) Spearman’s correlation plot of the CpG methylation values obtained from two spleen fresh frozen (FF) samples when compared with their consecutive sections that were preserved as formalin-fixed paraffin-embedded (FFPE). (d) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse cell lines C2C12, HAFTL, and P19 upon the use of the demethylating agent 5-aza-2’-deoxycytidine (dAZA). (e) Correlation plot of the CpG methylation values to show DNA hypomethylation events in the mouse embryonic stem cells upon genetic knock-out of the maintenance DNA methyltransferase Dnmt1. ..
Genome Wide:Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy
Article Snippet: .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, we performed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
Article Title: Epigenetic state determines the in vivo efficacy of STING agonist therapy.
Article Snippet: .. To test this, weperformed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNAmethyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine). .. To test this, weperformed genome-wide DNA methylation profiling using the Infinium Mouse Methylation BeadChip microarray in B16-F10 and Yumm1.7 melanoma cell lines before and after their treatment with DNAmethyltransferase inhibitor 5-aza-2’-deoxycytidine (5AZADC, decitabine).
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