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dna methylation microarray data infinium human methylation 450k beadchip  (INFINIUM Inc)

 
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    INFINIUM Inc dna methylation microarray data infinium human methylation 450k beadchip
    Dna Methylation Microarray Data Infinium Human Methylation 450k Beadchip, 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/human+dna+methylation+450k+microarray/infinium+humanmethylation450+beadchip/pm38067107-50-15-14
    Average 90 stars, based on 1 article reviews
    dna methylation microarray data infinium human methylation 450k beadchip - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    DNA Methylation Assay:

    Article Title: Invited Speakers
    Article Snippet: .. DNA methylation was measured in circulating white blood cells by a microarray strategy (Infinium Human Methylation 450K BeadChips). ..

    Article Title: Nutritional Epigenomics and Age-Related Disease
    Article Snippet: .. Although commonly used methods including HPLC-UV, LC-MS/MS, methyl acceptance assay, and pyrosequencing are still useful in analyses of DNA methylation, novel technologies such as the Infinium HumanMethylation450K BeadChip array (450K) or the Infinium MethylationEPIC BeadChip (850K) microarray provide higher resolution for analyzing DNA methylation on a genome-wide scale ( , ). .. Although not offering as much genome coverage as whole-genome bisulfite sequencing (WGBS), the Illumina arrays analyze a significant proportion of total sites for DNA methylation at 853,307 CpG sites (EPIC/850K) and 485,764 CpG sites (450K) across the human genome.

    Article Title: DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions.
    Article Snippet: .. 04 58 ) Th is pa pe r h as b ee n pe er ‐re vi ew ed a nd a cc ep te d fo r p ub lic at io n, b ut h as y et to u nd er go co py ed iti ng a nd p ro of co rr ec tio n. T he fi na l p ub lis he d ve rs io n m ay d iff er fr om th is pr oo f. Supplementary Methods Quality control and data processing of DNA methylation microarray Data from the Infinium Human Methylation 450K BeadChip methylation platform were analyzed using a combination of R and Bioconductor packages (https://www.bioconductor.org/). ..

    Article Title: Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain
    Article Snippet: .. DNA Methylation Analysis Infinium HumanMethylation 450k BeadChip Array DNA was purified from human brain samples or fluorescence-activated nuclear sorting (FANS)-sorted nuclei using the DNeasy Blood & Tissue kit (Qiagen) and bisulfite converted using EZ DNA methylation Gold kit (Zymo Research) according to manufacturers’ instructions. .. Methylation profiling was performed using Infinium HumanMethylation450 BeadChip assay (Illumina) by The SNP&SEQ Technology Platform at Science for Life Laboratory (Sweden).

    Article Title: Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene.
    Article Snippet: After performing immunostaining with anti β-amyloid and anti p-tau antibodies, the hippocampal sections were examined and representative images were analyzed with ImageJ software v1.52d to obtain an average quantitative measure for each section and patient (Supplementary Figure S1). .. In this study, we used our previous DNA methylation microarray data obtained by the Infinium Human Methylation 450K BeadChip (450K array) [11]. ..

    Microarray:

    Article Title: Invited Speakers
    Article Snippet: .. DNA methylation was measured in circulating white blood cells by a microarray strategy (Infinium Human Methylation 450K BeadChips). ..

    Article Title: IUNS. 21st International Congress of Nutrition. Buenos Aires, Argentina, October 15-20, 2017: Abstracts.
    Article Snippet: .. DNA from white blood cells was hybridized in an Infinium Human 450K methylation microarray. ..

    Article Title: Nutritional Epigenomics and Age-Related Disease
    Article Snippet: .. Although commonly used methods including HPLC-UV, LC-MS/MS, methyl acceptance assay, and pyrosequencing are still useful in analyses of DNA methylation, novel technologies such as the Infinium HumanMethylation450K BeadChip array (450K) or the Infinium MethylationEPIC BeadChip (850K) microarray provide higher resolution for analyzing DNA methylation on a genome-wide scale ( , ). .. Although not offering as much genome coverage as whole-genome bisulfite sequencing (WGBS), the Illumina arrays analyze a significant proportion of total sites for DNA methylation at 853,307 CpG sites (EPIC/850K) and 485,764 CpG sites (450K) across the human genome.

    Article Title: DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions.
    Article Snippet: .. 04 58 ) Th is pa pe r h as b ee n pe er ‐re vi ew ed a nd a cc ep te d fo r p ub lic at io n, b ut h as y et to u nd er go co py ed iti ng a nd p ro of co rr ec tio n. T he fi na l p ub lis he d ve rs io n m ay d iff er fr om th is pr oo f. Supplementary Methods Quality control and data processing of DNA methylation microarray Data from the Infinium Human Methylation 450K BeadChip methylation platform were analyzed using a combination of R and Bioconductor packages (https://www.bioconductor.org/). ..

    Article Title: Advance and challenge of DNA methylation as cancer biomarkers for risk stratification, screening and early detection
    Article Snippet: .. For instance, whole genome bisulfite sequencing (WGBS) and nanopore sequencing provide single-base resolution, while WGBS and methylation arrays (such as Infinium Human Methylation family of microarray-based methylation assays: 450K , 850 K, and 935 K) are suitable for whole-genome or large-scale studies. ..

    Article Title: Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene.
    Article Snippet: After performing immunostaining with anti β-amyloid and anti p-tau antibodies, the hippocampal sections were examined and representative images were analyzed with ImageJ software v1.52d to obtain an average quantitative measure for each section and patient (Supplementary Figure S1). .. In this study, we used our previous DNA methylation microarray data obtained by the Infinium Human Methylation 450K BeadChip (450K array) [11]. ..

    Methylation:

    Article Title: Invited Speakers
    Article Snippet: .. DNA methylation was measured in circulating white blood cells by a microarray strategy (Infinium Human Methylation 450K BeadChips). ..

    Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming
    Article Snippet: Rong et al 2015 Ref. 59 , GDM N= 36 Control N = 40 Nanjing, China , GDM diagnosed with glucose following 2h post-OGTT (2nd trimester, wk 24–28 , NimbleGen microarray Bisulfite DNA pyrosequencing , Bisulfite pyrosequencing used to validate array results for RETN, GLUT3, PPARa and RBP4 Non-adjusted one-way ANOVA. No FDR or Bonferroni adjustment or replication. , 6,641 DMRs (3,320 genes) DMGs enriched for pathways related to cell growth/regulation, immune/inflammatory responses and nervous system development. Technical validation of 3 metabolic genes GLUT3 , Resistin and PPARα . Differences in placenta mRNA between GDM and controls observed for GLUT3 and RETN .. .. Binder et al 2015 Ref. 60 , N=82 GDM N=41 Controls N=41 Harvard Epigenetic Birth Cohort (HEBC) Boston, MA USA & RICHS cohort Providence, RI, USA , GDM cases (GDM diagnosis excluded preexisting hypertension or diabetes) Controls (no GDM, no pregnancy-induced hypertension/preeclampsia, no previous hypertension or diabetes) , 450K Infinium Methylation BeadChip Array Bisulfite DNA Pyrosequencing for validation , Site-specific methylation modeled adjusting for maternal age (years), pre-pregnancy BMI (kg/m 2 ), infant sex, maternal smoking, and independent surrogate variables to assess technical variation in the methylation data. FDR to correct P values for multiple testing. Selected results tested for replication in an independent cohort (RICHS) , 78 DMRs (P <0.001) Findings in the MHC region partially validated in an independent cohort (RICHS). MHC transcripts also different between GDM compared to non-GDM placentas.. .. Cardenas et al 2018 Ref. 65 , N= 448 French-Canadian Canada Gen3G Birth Cohort Sherbrooke, Quebec , Maternal glucose following 2h post-OGTT test (2nd trimester, wk 24–28) , 850K Infinium Methylation BeadChip EPIC Array Bisulfite DNA Pyrosequencing , Robust linear regression models adjusted for maternal age, BMI, parity, smoking during pregnancy, gestational age, sex and the first 10 principal components estimated from a reference-free cell-type heterogeneity method as proxy for cellular heterogeneity. P-values adjusted with FDR at 5% (q-value<0.05) Bisulfite DNA pyrosequencing for replication in another smaller population (N=65 to 108). , Seven CpG sites (q<0.05) associated with ↑ 1 mMol/L 2h-glucose postOGTT: TNFRSF1B (cg26189983) 1.22% ↑ methylation PDE4B (cg07734160, cg13866577, cg03442467, cg13349623) ↓ methylation (−0.58 to −1.16%) BLM (cg20254265) −0.63% ↓ methylation LDLR (cg08483713) −0.27% ↓ methylation. PDE4B methylation (cg03442467 gene body/TSS200) correlated with PDE4B ↑ expression (r=0.31; P=1.81×10 −3 ), TNFRSF1B methylation (cg26189983) correlated with expression (r= −0.24; P=0.013). LDLR methylation (cg08483713 gene body) associated with ↑ expression (r=0.32, P=9.62×10 −4 ).

    Article Title: IUNS. 21st International Congress of Nutrition. Buenos Aires, Argentina, October 15-20, 2017: Abstracts.
    Article Snippet: .. DNA from white blood cells was hybridized in an Infinium Human 450K methylation microarray. ..

    Article Title: DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions.
    Article Snippet: .. 04 58 ) Th is pa pe r h as b ee n pe er ‐re vi ew ed a nd a cc ep te d fo r p ub lic at io n, b ut h as y et to u nd er go co py ed iti ng a nd p ro of co rr ec tio n. T he fi na l p ub lis he d ve rs io n m ay d iff er fr om th is pr oo f. Supplementary Methods Quality control and data processing of DNA methylation microarray Data from the Infinium Human Methylation 450K BeadChip methylation platform were analyzed using a combination of R and Bioconductor packages (https://www.bioconductor.org/). ..

    Article Title: Advance and challenge of DNA methylation as cancer biomarkers for risk stratification, screening and early detection
    Article Snippet: .. For instance, whole genome bisulfite sequencing (WGBS) and nanopore sequencing provide single-base resolution, while WGBS and methylation arrays (such as Infinium Human Methylation family of microarray-based methylation assays: 450K , 850 K, and 935 K) are suitable for whole-genome or large-scale studies. ..

    Article Title: Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene.
    Article Snippet: After performing immunostaining with anti β-amyloid and anti p-tau antibodies, the hippocampal sections were examined and representative images were analyzed with ImageJ software v1.52d to obtain an average quantitative measure for each section and patient (Supplementary Figure S1). .. In this study, we used our previous DNA methylation microarray data obtained by the Infinium Human Methylation 450K BeadChip (450K array) [11]. ..

    Biomarker Discovery:

    Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming
    Article Snippet: Rong et al 2015 Ref. 59 , GDM N= 36 Control N = 40 Nanjing, China , GDM diagnosed with glucose following 2h post-OGTT (2nd trimester, wk 24–28 , NimbleGen microarray Bisulfite DNA pyrosequencing , Bisulfite pyrosequencing used to validate array results for RETN, GLUT3, PPARa and RBP4 Non-adjusted one-way ANOVA. No FDR or Bonferroni adjustment or replication. , 6,641 DMRs (3,320 genes) DMGs enriched for pathways related to cell growth/regulation, immune/inflammatory responses and nervous system development. Technical validation of 3 metabolic genes GLUT3 , Resistin and PPARα . Differences in placenta mRNA between GDM and controls observed for GLUT3 and RETN .. .. Binder et al 2015 Ref. 60 , N=82 GDM N=41 Controls N=41 Harvard Epigenetic Birth Cohort (HEBC) Boston, MA USA & RICHS cohort Providence, RI, USA , GDM cases (GDM diagnosis excluded preexisting hypertension or diabetes) Controls (no GDM, no pregnancy-induced hypertension/preeclampsia, no previous hypertension or diabetes) , 450K Infinium Methylation BeadChip Array Bisulfite DNA Pyrosequencing for validation , Site-specific methylation modeled adjusting for maternal age (years), pre-pregnancy BMI (kg/m 2 ), infant sex, maternal smoking, and independent surrogate variables to assess technical variation in the methylation data. FDR to correct P values for multiple testing. Selected results tested for replication in an independent cohort (RICHS) , 78 DMRs (P <0.001) Findings in the MHC region partially validated in an independent cohort (RICHS). MHC transcripts also different between GDM compared to non-GDM placentas.. .. Cardenas et al 2018 Ref. 65 , N= 448 French-Canadian Canada Gen3G Birth Cohort Sherbrooke, Quebec , Maternal glucose following 2h post-OGTT test (2nd trimester, wk 24–28) , 850K Infinium Methylation BeadChip EPIC Array Bisulfite DNA Pyrosequencing , Robust linear regression models adjusted for maternal age, BMI, parity, smoking during pregnancy, gestational age, sex and the first 10 principal components estimated from a reference-free cell-type heterogeneity method as proxy for cellular heterogeneity. P-values adjusted with FDR at 5% (q-value<0.05) Bisulfite DNA pyrosequencing for replication in another smaller population (N=65 to 108). , Seven CpG sites (q<0.05) associated with ↑ 1 mMol/L 2h-glucose postOGTT: TNFRSF1B (cg26189983) 1.22% ↑ methylation PDE4B (cg07734160, cg13866577, cg03442467, cg13349623) ↓ methylation (−0.58 to −1.16%) BLM (cg20254265) −0.63% ↓ methylation LDLR (cg08483713) −0.27% ↓ methylation. PDE4B methylation (cg03442467 gene body/TSS200) correlated with PDE4B ↑ expression (r=0.31; P=1.81×10 −3 ), TNFRSF1B methylation (cg26189983) correlated with expression (r= −0.24; P=0.013). LDLR methylation (cg08483713 gene body) associated with ↑ expression (r=0.32, P=9.62×10 −4 ).

    Immunopeptidomics:

    Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming
    Article Snippet: Rong et al 2015 Ref. 59 , GDM N= 36 Control N = 40 Nanjing, China , GDM diagnosed with glucose following 2h post-OGTT (2nd trimester, wk 24–28 , NimbleGen microarray Bisulfite DNA pyrosequencing , Bisulfite pyrosequencing used to validate array results for RETN, GLUT3, PPARa and RBP4 Non-adjusted one-way ANOVA. No FDR or Bonferroni adjustment or replication. , 6,641 DMRs (3,320 genes) DMGs enriched for pathways related to cell growth/regulation, immune/inflammatory responses and nervous system development. Technical validation of 3 metabolic genes GLUT3 , Resistin and PPARα . Differences in placenta mRNA between GDM and controls observed for GLUT3 and RETN .. .. Binder et al 2015 Ref. 60 , N=82 GDM N=41 Controls N=41 Harvard Epigenetic Birth Cohort (HEBC) Boston, MA USA & RICHS cohort Providence, RI, USA , GDM cases (GDM diagnosis excluded preexisting hypertension or diabetes) Controls (no GDM, no pregnancy-induced hypertension/preeclampsia, no previous hypertension or diabetes) , 450K Infinium Methylation BeadChip Array Bisulfite DNA Pyrosequencing for validation , Site-specific methylation modeled adjusting for maternal age (years), pre-pregnancy BMI (kg/m 2 ), infant sex, maternal smoking, and independent surrogate variables to assess technical variation in the methylation data. FDR to correct P values for multiple testing. Selected results tested for replication in an independent cohort (RICHS) , 78 DMRs (P <0.001) Findings in the MHC region partially validated in an independent cohort (RICHS). MHC transcripts also different between GDM compared to non-GDM placentas.. .. Cardenas et al 2018 Ref. 65 , N= 448 French-Canadian Canada Gen3G Birth Cohort Sherbrooke, Quebec , Maternal glucose following 2h post-OGTT test (2nd trimester, wk 24–28) , 850K Infinium Methylation BeadChip EPIC Array Bisulfite DNA Pyrosequencing , Robust linear regression models adjusted for maternal age, BMI, parity, smoking during pregnancy, gestational age, sex and the first 10 principal components estimated from a reference-free cell-type heterogeneity method as proxy for cellular heterogeneity. P-values adjusted with FDR at 5% (q-value<0.05) Bisulfite DNA pyrosequencing for replication in another smaller population (N=65 to 108). , Seven CpG sites (q<0.05) associated with ↑ 1 mMol/L 2h-glucose postOGTT: TNFRSF1B (cg26189983) 1.22% ↑ methylation PDE4B (cg07734160, cg13866577, cg03442467, cg13349623) ↓ methylation (−0.58 to −1.16%) BLM (cg20254265) −0.63% ↓ methylation LDLR (cg08483713) −0.27% ↓ methylation. PDE4B methylation (cg03442467 gene body/TSS200) correlated with PDE4B ↑ expression (r=0.31; P=1.81×10 −3 ), TNFRSF1B methylation (cg26189983) correlated with expression (r= −0.24; P=0.013). LDLR methylation (cg08483713 gene body) associated with ↑ expression (r=0.32, P=9.62×10 −4 ).

    High Performance Liquid Chromatography:

    Article Title: Nutritional Epigenomics and Age-Related Disease
    Article Snippet: .. Although commonly used methods including HPLC-UV, LC-MS/MS, methyl acceptance assay, and pyrosequencing are still useful in analyses of DNA methylation, novel technologies such as the Infinium HumanMethylation450K BeadChip array (450K) or the Infinium MethylationEPIC BeadChip (850K) microarray provide higher resolution for analyzing DNA methylation on a genome-wide scale ( , ). .. Although not offering as much genome coverage as whole-genome bisulfite sequencing (WGBS), the Illumina arrays analyze a significant proportion of total sites for DNA methylation at 853,307 CpG sites (EPIC/850K) and 485,764 CpG sites (450K) across the human genome.

    Genome Wide:

    Article Title: Nutritional Epigenomics and Age-Related Disease
    Article Snippet: .. Although commonly used methods including HPLC-UV, LC-MS/MS, methyl acceptance assay, and pyrosequencing are still useful in analyses of DNA methylation, novel technologies such as the Infinium HumanMethylation450K BeadChip array (450K) or the Infinium MethylationEPIC BeadChip (850K) microarray provide higher resolution for analyzing DNA methylation on a genome-wide scale ( , ). .. Although not offering as much genome coverage as whole-genome bisulfite sequencing (WGBS), the Illumina arrays analyze a significant proportion of total sites for DNA methylation at 853,307 CpG sites (EPIC/850K) and 485,764 CpG sites (450K) across the human genome.

    Control:

    Article Title: DNA Methylation-Based Method to Differentiate Malignant from Benign Thyroid Lesions.
    Article Snippet: .. 04 58 ) Th is pa pe r h as b ee n pe er ‐re vi ew ed a nd a cc ep te d fo r p ub lic at io n, b ut h as y et to u nd er go co py ed iti ng a nd p ro of co rr ec tio n. T he fi na l p ub lis he d ve rs io n m ay d iff er fr om th is pr oo f. Supplementary Methods Quality control and data processing of DNA methylation microarray Data from the Infinium Human Methylation 450K BeadChip methylation platform were analyzed using a combination of R and Bioconductor packages (https://www.bioconductor.org/). ..

    Methylation Sequencing:

    Article Title: Advance and challenge of DNA methylation as cancer biomarkers for risk stratification, screening and early detection
    Article Snippet: .. For instance, whole genome bisulfite sequencing (WGBS) and nanopore sequencing provide single-base resolution, while WGBS and methylation arrays (such as Infinium Human Methylation family of microarray-based methylation assays: 450K , 850 K, and 935 K) are suitable for whole-genome or large-scale studies. ..

    Nanopore Sequencing:

    Article Title: Advance and challenge of DNA methylation as cancer biomarkers for risk stratification, screening and early detection
    Article Snippet: .. For instance, whole genome bisulfite sequencing (WGBS) and nanopore sequencing provide single-base resolution, while WGBS and methylation arrays (such as Infinium Human Methylation family of microarray-based methylation assays: 450K , 850 K, and 935 K) are suitable for whole-genome or large-scale studies. ..

    Purification:

    Article Title: Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain
    Article Snippet: .. DNA Methylation Analysis Infinium HumanMethylation 450k BeadChip Array DNA was purified from human brain samples or fluorescence-activated nuclear sorting (FANS)-sorted nuclei using the DNeasy Blood & Tissue kit (Qiagen) and bisulfite converted using EZ DNA methylation Gold kit (Zymo Research) according to manufacturers’ instructions. .. Methylation profiling was performed using Infinium HumanMethylation450 BeadChip assay (Illumina) by The SNP&SEQ Technology Platform at Science for Life Laboratory (Sweden).

    Fluorescence:

    Article Title: Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain
    Article Snippet: .. DNA Methylation Analysis Infinium HumanMethylation 450k BeadChip Array DNA was purified from human brain samples or fluorescence-activated nuclear sorting (FANS)-sorted nuclei using the DNeasy Blood & Tissue kit (Qiagen) and bisulfite converted using EZ DNA methylation Gold kit (Zymo Research) according to manufacturers’ instructions. .. Methylation profiling was performed using Infinium HumanMethylation450 BeadChip assay (Illumina) by The SNP&SEQ Technology Platform at Science for Life Laboratory (Sweden).



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    Genes with significantly different <t>DNA</t> methylation in one or more CpG sites in non-polymorphic regions. ( a ) List of 18 genes that have one of more CpG sites in non-polymorphic regions with difference in methylation ≥20%. DCAF6 and ZNF714 , highlighted orange, have variable copy number in genome. ( b ) Proportion of the locations of CpG sites in the 18 genes. TSS, transcription start site; TSS1500, the sequence region from −200 to −1,500 nucleotides upstream of the transcription start site; TSS200, the region from −200 nucleotides upstream to the TSS itself; UTR, untranslated region. ( c ) TaqMan Copy Number Assays for DCAF6 showed that among 14 donors, four have one copy of the gene (N2, N6, N7 and O4), five have two copies (N1, N3, N4, N5, and O1) and also five have three copies (O2, O3, O5, O6, and O7). All four WJ MSC samples that showed significantly different DCAF6 DNA methylation (*) originated from the donors that have three copies of the gene (O2, O3, O6, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( d and e ) Expression gene array did not detect significant difference DCAF6 mRNA expression in any of the samples indicating that duplicated DCAF6 genes might not be functional. ( f ) TaqMan Copy Number Assays for ZNF714 showed that all non-obese and obese donors have two copies of the ZNF714 gene. *Five donors that had significantly different DNA methylation of all CpG sites in ZNF714 (O1, O2, O4, O5, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( g and h ) Expression gene array did not detect significant difference ZNF714 mRNA expression in any of the samples indicating that the extra copy of ZNF714 gene might be either functional or not in all donors uniformly. ( i ) The mRNA expression levels of 16 genes showed no differences in the obese and non-obese groups. The Y axis represents the log2 of the normalized intensity values. The single exception was the PNPLA7 gene, which showed higher expression in the non-obese group than in the obese group (**p ≤ 0.01), the adjusted p-values from Linear Models for <t>Microarray</t> and RNA-Seq Data (limma) statistical test , .
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    Technical <t>DNA</t> <t>methylation</t> validation. (A) Scatter plot of DNA methylation levels obtained by Infinium Human Methylation <t>450k</t> BeadChip (Illumina Inc., San Diego, CA) (Y-axis) and bisulfite pyrosequencing (X-axis) (n = 11). A highly significant correlation (P < 0.001, R 2 = 0.978 and R 2 = 0.968, respectably) between <t>microarray</t> and pyrosequencing data was observed. Example of pyrograms with methylated (B) and unmethylated (C) cytosines.
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    Image Search Results


    Genes with significantly different DNA methylation in one or more CpG sites in non-polymorphic regions. ( a ) List of 18 genes that have one of more CpG sites in non-polymorphic regions with difference in methylation ≥20%. DCAF6 and ZNF714 , highlighted orange, have variable copy number in genome. ( b ) Proportion of the locations of CpG sites in the 18 genes. TSS, transcription start site; TSS1500, the sequence region from −200 to −1,500 nucleotides upstream of the transcription start site; TSS200, the region from −200 nucleotides upstream to the TSS itself; UTR, untranslated region. ( c ) TaqMan Copy Number Assays for DCAF6 showed that among 14 donors, four have one copy of the gene (N2, N6, N7 and O4), five have two copies (N1, N3, N4, N5, and O1) and also five have three copies (O2, O3, O5, O6, and O7). All four WJ MSC samples that showed significantly different DCAF6 DNA methylation (*) originated from the donors that have three copies of the gene (O2, O3, O6, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( d and e ) Expression gene array did not detect significant difference DCAF6 mRNA expression in any of the samples indicating that duplicated DCAF6 genes might not be functional. ( f ) TaqMan Copy Number Assays for ZNF714 showed that all non-obese and obese donors have two copies of the ZNF714 gene. *Five donors that had significantly different DNA methylation of all CpG sites in ZNF714 (O1, O2, O4, O5, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( g and h ) Expression gene array did not detect significant difference ZNF714 mRNA expression in any of the samples indicating that the extra copy of ZNF714 gene might be either functional or not in all donors uniformly. ( i ) The mRNA expression levels of 16 genes showed no differences in the obese and non-obese groups. The Y axis represents the log2 of the normalized intensity values. The single exception was the PNPLA7 gene, which showed higher expression in the non-obese group than in the obese group (**p ≤ 0.01), the adjusted p-values from Linear Models for Microarray and RNA-Seq Data (limma) statistical test , .

    Journal: Scientific Reports

    Article Title: Effects of maternal obesity on Wharton’s Jelly mesenchymal stromal cells

    doi: 10.1038/s41598-017-18034-1

    Figure Lengend Snippet: Genes with significantly different DNA methylation in one or more CpG sites in non-polymorphic regions. ( a ) List of 18 genes that have one of more CpG sites in non-polymorphic regions with difference in methylation ≥20%. DCAF6 and ZNF714 , highlighted orange, have variable copy number in genome. ( b ) Proportion of the locations of CpG sites in the 18 genes. TSS, transcription start site; TSS1500, the sequence region from −200 to −1,500 nucleotides upstream of the transcription start site; TSS200, the region from −200 nucleotides upstream to the TSS itself; UTR, untranslated region. ( c ) TaqMan Copy Number Assays for DCAF6 showed that among 14 donors, four have one copy of the gene (N2, N6, N7 and O4), five have two copies (N1, N3, N4, N5, and O1) and also five have three copies (O2, O3, O5, O6, and O7). All four WJ MSC samples that showed significantly different DCAF6 DNA methylation (*) originated from the donors that have three copies of the gene (O2, O3, O6, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( d and e ) Expression gene array did not detect significant difference DCAF6 mRNA expression in any of the samples indicating that duplicated DCAF6 genes might not be functional. ( f ) TaqMan Copy Number Assays for ZNF714 showed that all non-obese and obese donors have two copies of the ZNF714 gene. *Five donors that had significantly different DNA methylation of all CpG sites in ZNF714 (O1, O2, O4, O5, and O7). Each sample bar represents the mean calculated copy number and error bars show the standard deviation for three replicates. ( g and h ) Expression gene array did not detect significant difference ZNF714 mRNA expression in any of the samples indicating that the extra copy of ZNF714 gene might be either functional or not in all donors uniformly. ( i ) The mRNA expression levels of 16 genes showed no differences in the obese and non-obese groups. The Y axis represents the log2 of the normalized intensity values. The single exception was the PNPLA7 gene, which showed higher expression in the non-obese group than in the obese group (**p ≤ 0.01), the adjusted p-values from Linear Models for Microarray and RNA-Seq Data (limma) statistical test , .

    Article Snippet: Methylation levels at >480,000 CpG sites throughout the genome were measured using the Infinium Human DNA Methylation 450k BeadChip microarray(Illumina) in triplicate, each array representing an independent bisulfite conversion of a donor sample; performed at the Genomics Facility of the Biomedical Research Centre at the Guy’s and St Thomas’ National Health Service Foundation Trust and King’s College London.

    Techniques: DNA Methylation Assay, Methylation, Sequencing, Standard Deviation, Expressing, Functional Assay, Microarray, RNA Sequencing Assay

    Technical DNA methylation validation. (A) Scatter plot of DNA methylation levels obtained by Infinium Human Methylation 450k BeadChip (Illumina Inc., San Diego, CA) (Y-axis) and bisulfite pyrosequencing (X-axis) (n = 11). A highly significant correlation (P < 0.001, R 2 = 0.978 and R 2 = 0.968, respectably) between microarray and pyrosequencing data was observed. Example of pyrograms with methylated (B) and unmethylated (C) cytosines.

    Journal: Genomics Data

    Article Title: DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights

    doi: 10.1016/j.gdata.2015.07.016

    Figure Lengend Snippet: Technical DNA methylation validation. (A) Scatter plot of DNA methylation levels obtained by Infinium Human Methylation 450k BeadChip (Illumina Inc., San Diego, CA) (Y-axis) and bisulfite pyrosequencing (X-axis) (n = 11). A highly significant correlation (P < 0.001, R 2 = 0.978 and R 2 = 0.968, respectably) between microarray and pyrosequencing data was observed. Example of pyrograms with methylated (B) and unmethylated (C) cytosines.

    Article Snippet: Microarray DNA methylation data (Infinium Human Methylation 450k BeadChip) were analyzed and associated with functional/regulatory genome annotation data, transcriptional profiles and clinico-biological parameters.

    Techniques: DNA Methylation Assay, Biomarker Discovery, Methylation, Microarray

    Journal: Genomics Data

    Article Title: DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights

    doi: 10.1016/j.gdata.2015.07.016

    Figure Lengend Snippet:

    Article Snippet: Microarray DNA methylation data (Infinium Human Methylation 450k BeadChip) were analyzed and associated with functional/regulatory genome annotation data, transcriptional profiles and clinico-biological parameters.

    Techniques: Methylation