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Genomic coverage of 12 <t>rmRRBS</t> libraries at different read depths stratified <t>by</t> <t>CpG</t> resort context. a The total number of CpG loci covered, b the number of discrete contexts in which at least one CpG locus is covered, c the proportion of exactly the same contexts from the Infinium HumanMethyaltion450 (450K) array for which at least once CpG locus was covered, and d the proportion of exactly the same contexts from the Infinium MethyaltionEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico . In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of CpG loci measured in each discrete region that was covered is stratified in columns by type of CpG context and in rows by rmRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K, and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each region. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Rmrrbs, supplied by INFINIUM Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/rmrrbs/pmc05642382-63-4-13?v=INFINIUM+Inc
Average 90 stars, based on 1 article reviews

rmrrbs - by Bioz Stars, 2026-07

90/100 stars

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1) Product Images from "Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans"

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

Journal: NPJ Genomic Medicine

doi: 10.1038/s41525-017-0012-9

Genomic coverage of 12 rmRRBS libraries at different read depths stratified by CpG resort context. a The total number of CpG loci covered, b the number of discrete contexts in which at least one CpG locus is covered, c the proportion of exactly the same contexts from the Infinium HumanMethyaltion450 (450K) array for which at least once CpG locus was covered, and d the proportion of exactly the same contexts from the Infinium MethyaltionEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico . In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of CpG loci measured in each discrete region that was covered is stratified in columns by type of CpG context and in rows by rmRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K, and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each region. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Figure Legend Snippet: Genomic coverage of 12 rmRRBS libraries at different read depths stratified by CpG resort context. a The total number of CpG loci covered, b the number of discrete contexts in which at least one CpG locus is covered, c the proportion of exactly the same contexts from the Infinium HumanMethyaltion450 (450K) array for which at least once CpG locus was covered, and d the proportion of exactly the same contexts from the Infinium MethyaltionEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico . In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of CpG loci measured in each discrete region that was covered is stratified in columns by type of CpG context and in rows by rmRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K, and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each region. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Techniques Used: In Silico

Genomic coverage of 12 rmRRBS libraries at different read depths stratified by four types of genes. a The total number of CpG loci covered b the number of genes in which at least one CpG locus is covered c the proportion of genes on the Infinium HumanMethyation450 (450K) array for which at least once CpG locus is covered, and d the proportion of genes on the Infinium MethyationEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico. In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of loci measured in each gene that was covered is stratified in columns by type of gene and in rows by mRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each gene. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Figure Legend Snippet: Genomic coverage of 12 rmRRBS libraries at different read depths stratified by four types of genes. a The total number of CpG loci covered b the number of genes in which at least one CpG locus is covered c the proportion of genes on the Infinium HumanMethyation450 (450K) array for which at least once CpG locus is covered, and d the proportion of genes on the Infinium MethyationEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico. In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of loci measured in each gene that was covered is stratified in columns by type of gene and in rows by mRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each gene. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Techniques Used: In Silico

Overlap in genomic coverage between different rmRRBS libraries. The number of CpG loci, CpG resort context-restricted genomic tiles up to 200 base pairs (200 bp tiles) or 2000 base pairs (2 kb tiles) in length, protein coding genes, cancer-associated genes, microRNA genes, and nuclear encoded genes related to mitochondrial function are plotted relative to the number of rmRRBS libraries in which exact matches overlap. Different color lines correspond rmRRBS read depth, ranging from ≥1× to ≥10× reads per CpG locus, 200 bp, 2 kb tile, or gene. For reference, horizontal lines indicate the number of CpG loci, tiles or genes covered by the Infinium HumanMethylation450 (450K; dark green) and the Infinium MethyationEPIC (850K; dark blue)

Figure Legend Snippet: Overlap in genomic coverage between different rmRRBS libraries. The number of CpG loci, CpG resort context-restricted genomic tiles up to 200 base pairs (200 bp tiles) or 2000 base pairs (2 kb tiles) in length, protein coding genes, cancer-associated genes, microRNA genes, and nuclear encoded genes related to mitochondrial function are plotted relative to the number of rmRRBS libraries in which exact matches overlap. Different color lines correspond rmRRBS read depth, ranging from ≥1× to ≥10× reads per CpG locus, 200 bp, 2 kb tile, or gene. For reference, horizontal lines indicate the number of CpG loci, tiles or genes covered by the Infinium HumanMethylation450 (450K; dark green) and the Infinium MethyationEPIC (850K; dark blue)

Techniques Used:

Reproducibility of rmRRBS DNA methylation measurements. The Pearson correlations between DNA methylation measurements for combined reads from all 12 libraries prepared under each of six different experimental conditions and reads from the individual 12 libraries prepared under that condition, stratified by CpG resort context, ranging from ≥1× to ≥10× reads for the individual library, are plotted for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Figure Legend Snippet: Reproducibility of rmRRBS DNA methylation measurements. The Pearson correlations between DNA methylation measurements for combined reads from all 12 libraries prepared under each of six different experimental conditions and reads from the individual 12 libraries prepared under that condition, stratified by CpG resort context, ranging from ≥1× to ≥10× reads for the individual library, are plotted for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Techniques Used: DNA Methylation Assay

Concordance of rmRRBS and Infinium DNA methylation measurements. The Pearson correlations between DNA methylation measurements from 12 rmRRBS libraries derived from ten different participants’ (labeled A–J) gDNA and DNA methylation measurements for the corresponding Infinium HumanMethylation450 (450K) data derived from the same ten participants’ gDNA is plotted from ≥1× to ≥10× rmRRBS reads. Results are stratified by CpG resort context and shown for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Figure Legend Snippet: Concordance of rmRRBS and Infinium DNA methylation measurements. The Pearson correlations between DNA methylation measurements from 12 rmRRBS libraries derived from ten different participants’ (labeled A–J) gDNA and DNA methylation measurements for the corresponding Infinium HumanMethylation450 (450K) data derived from the same ten participants’ gDNA is plotted from ≥1× to ≥10× rmRRBS reads. Results are stratified by CpG resort context and shown for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Techniques Used: DNA Methylation Assay, Derivative Assay, Labeling

Genotype and allele-specific DNA methylation are measured by rmRRBS but not the Infinium BeadChip. A diagram illustrating the position of the target region in H19 within the 11p15 imprinting region is shown at the top of the figure. The primary sequencing of DNA nucleotides appears at the bottom, with a G/T single nucleotide polymorphism (SNP) highlighted in a red box in the body of the figure. Monoallelic DNA methylation for the five CpG loci covered by rmRRBS, as well as overall DNA methylation for the single CpG locus covered by the Infinium HumanMethylation450 (450K) array, are shown for the six individuals (including one replicate of J) who were heterozygous for the G/T SNP with blue saturation of heatmap cells indicating DNA methylation levels. Predicted regulatory functions based on Epigenetic Roadmap chromatin state data is shown above the DNA methylation heatmaps

Figure Legend Snippet: Genotype and allele-specific DNA methylation are measured by rmRRBS but not the Infinium BeadChip. A diagram illustrating the position of the target region in H19 within the 11p15 imprinting region is shown at the top of the figure. The primary sequencing of DNA nucleotides appears at the bottom, with a G/T single nucleotide polymorphism (SNP) highlighted in a red box in the body of the figure. Monoallelic DNA methylation for the five CpG loci covered by rmRRBS, as well as overall DNA methylation for the single CpG locus covered by the Infinium HumanMethylation450 (450K) array, are shown for the six individuals (including one replicate of J) who were heterozygous for the G/T SNP with blue saturation of heatmap cells indicating DNA methylation levels. Predicted regulatory functions based on Epigenetic Roadmap chromatin state data is shown above the DNA methylation heatmaps

Techniques Used: DNA Methylation Assay, Sequencing

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Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Genomic coverage of 12 rmRRBS libraries at different read depths stratified by CpG resort context. a The total number of CpG loci covered, b the number of discrete contexts in which at least one CpG locus is covered, c the proportion of exactly the same contexts from the Infinium HumanMethyaltion450 (450K) array for which at least once CpG locus was covered, and d the proportion of exactly the same contexts from the Infinium MethyaltionEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico . In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of CpG loci measured in each discrete region that was covered is stratified in columns by type of CpG context and in rows by rmRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K, and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each region. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques: In Silico

Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Genomic coverage of 12 rmRRBS libraries at different read depths stratified by four types of genes. a The total number of CpG loci covered b the number of genes in which at least one CpG locus is covered c the proportion of genes on the Infinium HumanMethyation450 (450K) array for which at least once CpG locus is covered, and d the proportion of genes on the Infinium MethyationEPIC (850K) array for which at least once CpG locus is covered are plotted from ≥1× to ≥10× reads. In panels ( a )–( d ), the dark red horizontal lines indicate predicted RRBS genomic coverage, bioinformatically determined by performing RRBS in silico. In panels ( a ) and ( b ), the dark green horizontal lines indicate Infinium 450K genomic coverage, and the dark blue horizontal lines indicate Infinium 850K genomic coverage. ( e ) The distribution of the number of loci measured in each gene that was covered is stratified in columns by type of gene and in rows by mRRBS read depth, with CpG density distributions for in silico RRBS, the Infinium 450K and the Infinium 850K plotted together in the fourth row. The peak of the density is the mode, and indicates most common number of CpG loci measured in each gene. In all panels, unique individuals A through J appear as different colored lines where solid lines indicate normal cluster density and dotted lines indicated high cluster density

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques: In Silico

Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Overlap in genomic coverage between different rmRRBS libraries. The number of CpG loci, CpG resort context-restricted genomic tiles up to 200 base pairs (200 bp tiles) or 2000 base pairs (2 kb tiles) in length, protein coding genes, cancer-associated genes, microRNA genes, and nuclear encoded genes related to mitochondrial function are plotted relative to the number of rmRRBS libraries in which exact matches overlap. Different color lines correspond rmRRBS read depth, ranging from ≥1× to ≥10× reads per CpG locus, 200 bp, 2 kb tile, or gene. For reference, horizontal lines indicate the number of CpG loci, tiles or genes covered by the Infinium HumanMethylation450 (450K; dark green) and the Infinium MethyationEPIC (850K; dark blue)

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques:

Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Reproducibility of rmRRBS DNA methylation measurements. The Pearson correlations between DNA methylation measurements for combined reads from all 12 libraries prepared under each of six different experimental conditions and reads from the individual 12 libraries prepared under that condition, stratified by CpG resort context, ranging from ≥1× to ≥10× reads for the individual library, are plotted for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques: DNA Methylation Assay

Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Concordance of rmRRBS and Infinium DNA methylation measurements. The Pearson correlations between DNA methylation measurements from 12 rmRRBS libraries derived from ten different participants’ (labeled A–J) gDNA and DNA methylation measurements for the corresponding Infinium HumanMethylation450 (450K) data derived from the same ten participants’ gDNA is plotted from ≥1× to ≥10× rmRRBS reads. Results are stratified by CpG resort context and shown for CpG loci, 200 base pair genomic tiles (200 bp tiles), and 2000 base pair genomic tiles (2 kb tiles)

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques: DNA Methylation Assay, Derivative Assay, Labeling

Journal: NPJ Genomic Medicine

Article Title: Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans

doi: 10.1038/s41525-017-0012-9

Figure Lengend Snippet: Genotype and allele-specific DNA methylation are measured by rmRRBS but not the Infinium BeadChip. A diagram illustrating the position of the target region in H19 within the 11p15 imprinting region is shown at the top of the figure. The primary sequencing of DNA nucleotides appears at the bottom, with a G/T single nucleotide polymorphism (SNP) highlighted in a red box in the body of the figure. Monoallelic DNA methylation for the five CpG loci covered by rmRRBS, as well as overall DNA methylation for the single CpG locus covered by the Infinium HumanMethylation450 (450K) array, are shown for the six individuals (including one replicate of J) who were heterozygous for the G/T SNP with blue saturation of heatmap cells indicating DNA methylation levels. Predicted regulatory functions based on Epigenetic Roadmap chromatin state data is shown above the DNA methylation heatmaps

Article Snippet: Regardless of genomic context, rmRRBS covered more CpG loci per region than the Infinium arrays (Figs. e, ).

Techniques: DNA Methylation Assay, Sequencing

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