ez dna methylation gold kit  (Zymo Research)


Bioz Verified Symbol Zymo Research is a verified supplier
Bioz Manufacturer Symbol Zymo Research manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    EZ DNA Methylation Gold Kit
    Description:
    The EZ DNA Methylation Gold Kit is a refinement of our popular EZ DNA Methylation kit and uses heat denaturation instead of chemical denaturation of the input DNA This allows for the denaturation and bisulfite conversion steps to be consolidated into one step leading to a much reduced incubation time Recovered bisulfite converted DNA is ideal for PCR amplification for downstream analyses including endonuclease digestion sequencing microarrays etc
    Catalog Number:
    d5006
    Price:
    None
    Category:
    Life Science Reagents and Media
    Applications:
    Bisulfite Conversion
    Size:
    50 units
    Buy from Supplier


    Structured Review

    Zymo Research ez dna methylation gold kit
    EZ DNA Methylation Gold Kit
    The EZ DNA Methylation Gold Kit is a refinement of our popular EZ DNA Methylation kit and uses heat denaturation instead of chemical denaturation of the input DNA This allows for the denaturation and bisulfite conversion steps to be consolidated into one step leading to a much reduced incubation time Recovered bisulfite converted DNA is ideal for PCR amplification for downstream analyses including endonuclease digestion sequencing microarrays etc
    https://www.bioz.com/result/ez dna methylation gold kit/product/Zymo Research
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ez dna methylation gold kit - by Bioz Stars, 2021-03
    99/100 stars

    Images

    1) Product Images from "DNA methyltransferase inhibition reduces inflammation-induced colon tumorigenesis"

    Article Title: DNA methyltransferase inhibition reduces inflammation-induced colon tumorigenesis

    Journal: Epigenetics

    doi: 10.1080/15592294.2019.1634986

    Tumours from DAC-treated mice have reduced inflammation-induced methylation changes . (a) Venn diagrams of the number of regions with significantly increased (upper panel) or decreased (lower panel) MBD-seq z-scores in the indicated tumour type relative to mock epithelium. (b) PCA analysis of MBD-seq z-scores of the 279 regions with DNA hypermethylation in one of the tumour groups relative to mock epithelium. Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. Prediction ellipses are such that with probability 0.95, a new observation from the same group will fall inside the ellipse. All tissue samples were collected 8 weeks after inoculation (N = 3 mock epithelia; N = 8 ETBF or ETBF/DAC tumours). (c) Unsupervised hierarchical clustering of regions (rows) and samples (columns) from b. Rows are centred; unit variance scaling is applied to rows. Both rows and columns are clustered using Euclidean distance and Ward linkage. The colour of each cell reflects the degree of DNA methylation. (d) qMSP of bisulfite treated DNA from indicated tissue in CpG islands of candidate genes. Mean ± SEM. N ≥ 6. * P
    Figure Legend Snippet: Tumours from DAC-treated mice have reduced inflammation-induced methylation changes . (a) Venn diagrams of the number of regions with significantly increased (upper panel) or decreased (lower panel) MBD-seq z-scores in the indicated tumour type relative to mock epithelium. (b) PCA analysis of MBD-seq z-scores of the 279 regions with DNA hypermethylation in one of the tumour groups relative to mock epithelium. Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. Prediction ellipses are such that with probability 0.95, a new observation from the same group will fall inside the ellipse. All tissue samples were collected 8 weeks after inoculation (N = 3 mock epithelia; N = 8 ETBF or ETBF/DAC tumours). (c) Unsupervised hierarchical clustering of regions (rows) and samples (columns) from b. Rows are centred; unit variance scaling is applied to rows. Both rows and columns are clustered using Euclidean distance and Ward linkage. The colour of each cell reflects the degree of DNA methylation. (d) qMSP of bisulfite treated DNA from indicated tissue in CpG islands of candidate genes. Mean ± SEM. N ≥ 6. * P

    Techniques Used: Mouse Assay, Methylation, DNA Methylation Assay

    Related Articles

    Methylation:

    Article Title: High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation
    Article Snippet: .. M.CviPI-methylated DNA was subjected to bisulfite conversion using a Zymo Research EZ DNA Methylation-Gold kit according to the manufacturer's direction. ..

    Article Title: A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation
    Article Snippet: .. Measurement of relative DNA methylation levels using MethyLight Genomic DNA was bisulfite-converted using an EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions. .. PCR primers and probes for MethyLight analyses were designed specifically for bisulfite-converted DNA (5′ to 3′ plus strand) using ABI Primer Express v3.

    Article Title: Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing
    Article Snippet: DNA extraction and bisulfite sequencingGenomic DNA (gDNA) was extracted form pelleted cells using DNeasy Blood and Tissue Kit (Qiagen, 69504). .. 500 ng of gDNA were bisulfite converted using EZ DNA Methylation-Gold Kit (Zymo Research, D5005). .. Amplification and cloningNested PCR was performed with appropriate primers (Supplementary Table S3) using OneTaq Hot Start DNA Polymerase (New England Biolabs, M0481) and OneTaq Standard Reaction Buffer (New England Biolabs, M0481).

    Article Title: Auxin‐activated MdARF5 induces the expression of ethylene biosynthetic genes to initiate apple fruit ripening
    Article Snippet: The intensity of the PCR product shift was measured using the c Series Capture Software. .. A BSP (bisulfite sequence PCR) assay was performed using the EZ DNA Methylation‐Gold Kit (catalog no. D5005; Zymo Research, Irvine, CA, USA), with 200 ng DNA used for the CT conversion step, and the rest of the protocol was according to the manufacturer’s instructions. ..

    Article Title: DNMT1 maintains the methylation of miR‐152‐3p to regulate TMSB10 expression, thereby affecting the biological characteristics of colorectal cancer cells. DNMT1 maintains the methylation of miR‐152‐3p to regulate TMSB10 expression, thereby affecting the biological characteristics of colorectal cancer cells
    Article Snippet: The gray value of each band was analyzed via ImageJ software. .. 2.7 Methylation‐specific PCR ( MSP )Genomic DNA was processed with EZ DNA Methylation‐Gold™ kit (Zymo Research, Orange, CA). .. PCR was performed with HotStar Taq polymerase (Qiagen).

    Article Title: Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas
    Article Snippet: .. CDKN2A and PTEN Promoter Methylation Specific PCR Purified genomic DNA from chordoma cases were bisulfite treated using the Zymo Research EZ DNA Methylation-Gold™. .. Promega Human Genomic DNA∶Male (Madison, WI) was used as the genomic unmethylated control.

    Article Title: EZH2-Inhibited MicroRNA-454-3p Promotes M2 Macrophage Polarization in Glioma
    Article Snippet: Initially, glioma DNA was extracted using BGenomic DNA Extraction Kit (Beijing Tiangen Biotech, Beijing, China), DNA concentration and purity were determined with ultraviolet spectrophotometry and stored in −80°C refrigerator for later use. .. MS-PCR was then conducted with the DNA Methylation-GoldTM kit (D5005, Zymo Research, Irvine, CA, United States). .. Briefly, 1 μg of DNA was subjected to bisulfite modification, and stored at −80°C for no longer than 1 month, followed by desulfurization and purification using reaction column.

    Pyrosequencing Assay:

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes
    Article Snippet: GATA3 transient silencing Cells were transfected with siRNAs (50 nM) against GATA3 , or a non-targeting siRNA negative control (Supplementary Table ; all synthesised by Sigma), using Lipofectamine 2000 transfection reagent (Invitrogen) and harvested after 72 hrs. .. Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen). .. Pyrosequencing assay 01 for GATA3 was PM00042273 (Qiagen); sequence analysed TTAATYGYGAGTATTAAGTYGGATTGGTYGGGGA, and assay 02 was PM00042280 (Qiagen); sequence analysed GATGTTTTTTAATTGGGTYGTTTAATAAYGGGA.

    DNA Methylation Assay:

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes
    Article Snippet: GATA3 transient silencing Cells were transfected with siRNAs (50 nM) against GATA3 , or a non-targeting siRNA negative control (Supplementary Table ; all synthesised by Sigma), using Lipofectamine 2000 transfection reagent (Invitrogen) and harvested after 72 hrs. .. Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen). .. Pyrosequencing assay 01 for GATA3 was PM00042273 (Qiagen); sequence analysed TTAATYGYGAGTATTAAGTYGGATTGGTYGGGGA, and assay 02 was PM00042280 (Qiagen); sequence analysed GATGTTTTTTAATTGGGTYGTTTAATAAYGGGA.

    Article Title: A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation
    Article Snippet: .. Measurement of relative DNA methylation levels using MethyLight Genomic DNA was bisulfite-converted using an EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions. .. PCR primers and probes for MethyLight analyses were designed specifically for bisulfite-converted DNA (5′ to 3′ plus strand) using ABI Primer Express v3.

    Amplification:

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes
    Article Snippet: GATA3 transient silencing Cells were transfected with siRNAs (50 nM) against GATA3 , or a non-targeting siRNA negative control (Supplementary Table ; all synthesised by Sigma), using Lipofectamine 2000 transfection reagent (Invitrogen) and harvested after 72 hrs. .. Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen). .. Pyrosequencing assay 01 for GATA3 was PM00042273 (Qiagen); sequence analysed TTAATYGYGAGTATTAAGTYGGATTGGTYGGGGA, and assay 02 was PM00042280 (Qiagen); sequence analysed GATGTTTTTTAATTGGGTYGTTTAATAAYGGGA.

    Polymerase Chain Reaction:

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes
    Article Snippet: GATA3 transient silencing Cells were transfected with siRNAs (50 nM) against GATA3 , or a non-targeting siRNA negative control (Supplementary Table ; all synthesised by Sigma), using Lipofectamine 2000 transfection reagent (Invitrogen) and harvested after 72 hrs. .. Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen). .. Pyrosequencing assay 01 for GATA3 was PM00042273 (Qiagen); sequence analysed TTAATYGYGAGTATTAAGTYGGATTGGTYGGGGA, and assay 02 was PM00042280 (Qiagen); sequence analysed GATGTTTTTTAATTGGGTYGTTTAATAAYGGGA.

    Article Title: Auxin‐activated MdARF5 induces the expression of ethylene biosynthetic genes to initiate apple fruit ripening
    Article Snippet: The intensity of the PCR product shift was measured using the c Series Capture Software. .. A BSP (bisulfite sequence PCR) assay was performed using the EZ DNA Methylation‐Gold Kit (catalog no. D5005; Zymo Research, Irvine, CA, USA), with 200 ng DNA used for the CT conversion step, and the rest of the protocol was according to the manufacturer’s instructions. ..

    Article Title: DNMT1 maintains the methylation of miR‐152‐3p to regulate TMSB10 expression, thereby affecting the biological characteristics of colorectal cancer cells. DNMT1 maintains the methylation of miR‐152‐3p to regulate TMSB10 expression, thereby affecting the biological characteristics of colorectal cancer cells
    Article Snippet: The gray value of each band was analyzed via ImageJ software. .. 2.7 Methylation‐specific PCR ( MSP )Genomic DNA was processed with EZ DNA Methylation‐Gold™ kit (Zymo Research, Orange, CA). .. PCR was performed with HotStar Taq polymerase (Qiagen).

    Article Title: Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas
    Article Snippet: .. CDKN2A and PTEN Promoter Methylation Specific PCR Purified genomic DNA from chordoma cases were bisulfite treated using the Zymo Research EZ DNA Methylation-Gold™. .. Promega Human Genomic DNA∶Male (Madison, WI) was used as the genomic unmethylated control.

    Sequencing:

    Article Title: Auxin‐activated MdARF5 induces the expression of ethylene biosynthetic genes to initiate apple fruit ripening
    Article Snippet: The intensity of the PCR product shift was measured using the c Series Capture Software. .. A BSP (bisulfite sequence PCR) assay was performed using the EZ DNA Methylation‐Gold Kit (catalog no. D5005; Zymo Research, Irvine, CA, USA), with 200 ng DNA used for the CT conversion step, and the rest of the protocol was according to the manufacturer’s instructions. ..

    Purification:

    Article Title: Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas
    Article Snippet: .. CDKN2A and PTEN Promoter Methylation Specific PCR Purified genomic DNA from chordoma cases were bisulfite treated using the Zymo Research EZ DNA Methylation-Gold™. .. Promega Human Genomic DNA∶Male (Madison, WI) was used as the genomic unmethylated control.

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Zymo Research ez dna methylation gold kit
    GATA3 <t>DNA</t> methylation and expression. ( A ) GATA3 sense (hatched bars) and antisense (unfilled bars) RNA expression assayed by QPCR, and DNA methylation levels (black bars) detected by <t>pyrosequencing,</t> in control tissues and neuroblastoma cell lines. RNA levels were normalized to endogenous levels of TBP and expressed relative to hNCC. DNA methylation was calculated as the average of the 01 and 02 pyrosequencing assays. ( B ) GATA3 protein levels assayed by Western blot in normal tissues (NT) and type-S, type-I, I + S and type-N neuroblastoma cell lines, with ACTIN as a loading control. Uncropped blots are shown in Supplementary Fig. S10 . ( C ) GATA3 sense RNA expression in DRG/SG cells treated with 2 μM AZA for 6 days. RNA levels were normalized to endogenous levels of TBP and expressed relative to control. Mean ± S.E.M of three experiments; *p
    Ez Dna Methylation Gold Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ez dna methylation gold kit/product/Zymo Research
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ez dna methylation gold kit - by Bioz Stars, 2021-03
    99/100 stars
      Buy from Supplier

    Image Search Results


    GATA3 DNA methylation and expression. ( A ) GATA3 sense (hatched bars) and antisense (unfilled bars) RNA expression assayed by QPCR, and DNA methylation levels (black bars) detected by pyrosequencing, in control tissues and neuroblastoma cell lines. RNA levels were normalized to endogenous levels of TBP and expressed relative to hNCC. DNA methylation was calculated as the average of the 01 and 02 pyrosequencing assays. ( B ) GATA3 protein levels assayed by Western blot in normal tissues (NT) and type-S, type-I, I + S and type-N neuroblastoma cell lines, with ACTIN as a loading control. Uncropped blots are shown in Supplementary Fig. S10 . ( C ) GATA3 sense RNA expression in DRG/SG cells treated with 2 μM AZA for 6 days. RNA levels were normalized to endogenous levels of TBP and expressed relative to control. Mean ± S.E.M of three experiments; *p

    Journal: Scientific Reports

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes

    doi: 10.1038/s41598-019-55382-6

    Figure Lengend Snippet: GATA3 DNA methylation and expression. ( A ) GATA3 sense (hatched bars) and antisense (unfilled bars) RNA expression assayed by QPCR, and DNA methylation levels (black bars) detected by pyrosequencing, in control tissues and neuroblastoma cell lines. RNA levels were normalized to endogenous levels of TBP and expressed relative to hNCC. DNA methylation was calculated as the average of the 01 and 02 pyrosequencing assays. ( B ) GATA3 protein levels assayed by Western blot in normal tissues (NT) and type-S, type-I, I + S and type-N neuroblastoma cell lines, with ACTIN as a loading control. Uncropped blots are shown in Supplementary Fig. S10 . ( C ) GATA3 sense RNA expression in DRG/SG cells treated with 2 μM AZA for 6 days. RNA levels were normalized to endogenous levels of TBP and expressed relative to control. Mean ± S.E.M of three experiments; *p

    Article Snippet: Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen).

    Techniques: DNA Methylation Assay, Expressing, RNA Expression, Real-time Polymerase Chain Reaction, Western Blot

    GATA3 DNA methylation in neuroblastoma. ( A ) GATA3 DNA methylation detected by MCIP. Black bars show the probe ratios derived from MCIP for hNCC and four neuroblastoma cell lines, positioned on the GATA3 CpG island promoter region, showing the sense and antisense transcripts and CpG island (CGI) (human genome build NCBI36/Hg18 visualised on the UCSC genome browser; http://genome.ucsc.edu ). The positions of the hypomethylated region and the two pyrosequencing assays (01 and 02) are shown in red at the top. ( B ) Dotboxplot of GATA3 antisense DNA methylation measured by pyrosequencing in normal tissues (NT, n = 4), neuroblastoma cell lines (Cell lines, n = 12), and neuroblastoma tumour tissue (NB tissue, n = 24), using the average of pyrosequencing assays 01 and 02; full results in C; *p

    Journal: Scientific Reports

    Article Title: Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes

    doi: 10.1038/s41598-019-55382-6

    Figure Lengend Snippet: GATA3 DNA methylation in neuroblastoma. ( A ) GATA3 DNA methylation detected by MCIP. Black bars show the probe ratios derived from MCIP for hNCC and four neuroblastoma cell lines, positioned on the GATA3 CpG island promoter region, showing the sense and antisense transcripts and CpG island (CGI) (human genome build NCBI36/Hg18 visualised on the UCSC genome browser; http://genome.ucsc.edu ). The positions of the hypomethylated region and the two pyrosequencing assays (01 and 02) are shown in red at the top. ( B ) Dotboxplot of GATA3 antisense DNA methylation measured by pyrosequencing in normal tissues (NT, n = 4), neuroblastoma cell lines (Cell lines, n = 12), and neuroblastoma tumour tissue (NB tissue, n = 24), using the average of pyrosequencing assays 01 and 02; full results in C; *p

    Article Snippet: Pyrosequencing assay of GATA3 DNA methylation DNA was bisulfite converted (EZ DNA Methylation Gold kit; Zymo Research), amplified with biotinylated primers (Qiagen) using a Pyromark PCR kit (Qiagen) and pyrosequenced on a PyroMark Q96 instrument (Qiagen).

    Techniques: DNA Methylation Assay, Derivative Assay

    T quantitative real-time PCR. Two primer/probe sets were used to quantitate T (6q27) and MCM7 (7q21.3-q22.1) (n = 3). Relative T ∶ MCM7 ratios were normalized against an average ratio established from ten non-chordoma DNA samples (normal). The normalized ratios were corrected for MCM7 copy number from array CGH data and approximate tumor percentage based on histological review. Corrected normalized ratios were multiplied by 2 to obtain the absolute T copy number. The dashed line represents a normal copy number of 2.

    Journal: PLoS ONE

    Article Title: Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas

    doi: 10.1371/journal.pone.0018846

    Figure Lengend Snippet: T quantitative real-time PCR. Two primer/probe sets were used to quantitate T (6q27) and MCM7 (7q21.3-q22.1) (n = 3). Relative T ∶ MCM7 ratios were normalized against an average ratio established from ten non-chordoma DNA samples (normal). The normalized ratios were corrected for MCM7 copy number from array CGH data and approximate tumor percentage based on histological review. Corrected normalized ratios were multiplied by 2 to obtain the absolute T copy number. The dashed line represents a normal copy number of 2.

    Article Snippet: CDKN2A and PTEN Promoter Methylation Specific PCR Purified genomic DNA from chordoma cases were bisulfite treated using the Zymo Research EZ DNA Methylation-Gold™.

    Techniques: Real-time Polymerase Chain Reaction

    CDKN2A and PTEN methylation specific PCR. Bisulfite-treated chordoma DNA samples were tested with methylation specific PCR to evaluate for hypermethylation of the CDKN2A and PTEN promoter regions. Two sets of unmethylated (U) and methylated (M) PCR primers were used for each target gene (bottom labels, MSP1 and MSP2). Unmethylated and methylated controls are shown along with results for case CH33. Results for other tested cases are summarized in Tables 3 and 4 under the CDKN2A and PTEN MSP1 and MSP2 columns. Tick marks on the left and right of each panel indicate 100, 200, 300, and 400 base pair sizes (bottom to top).

    Journal: PLoS ONE

    Article Title: Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas

    doi: 10.1371/journal.pone.0018846

    Figure Lengend Snippet: CDKN2A and PTEN methylation specific PCR. Bisulfite-treated chordoma DNA samples were tested with methylation specific PCR to evaluate for hypermethylation of the CDKN2A and PTEN promoter regions. Two sets of unmethylated (U) and methylated (M) PCR primers were used for each target gene (bottom labels, MSP1 and MSP2). Unmethylated and methylated controls are shown along with results for case CH33. Results for other tested cases are summarized in Tables 3 and 4 under the CDKN2A and PTEN MSP1 and MSP2 columns. Tick marks on the left and right of each panel indicate 100, 200, 300, and 400 base pair sizes (bottom to top).

    Article Snippet: CDKN2A and PTEN Promoter Methylation Specific PCR Purified genomic DNA from chordoma cases were bisulfite treated using the Zymo Research EZ DNA Methylation-Gold™.

    Techniques: Methylation, Polymerase Chain Reaction

    Validation of top-ranked DMP cg20475486 using a clinical biomarker assay. Replication of the top-ranked DMP associated with aGVHD severity, cg20475486, using a semi-quantitative DNA methylation assay. a Box-and-whisker plot of DNA methylation values in graft donors in T cell-depleted HSCT (initial discovery cohort). We replicated the DNA hypomethylation phenotype in HSCT donors matched to recipients with severe aGVHD compared to no/mild aGVHD ( P = 0.039, Wilcoxon rank-sum test). b At a relative DNA methylation threshold of 8.295 (dotted line), the AUC was 0.74 with a maximal specificity and sensitivity of 0.75 and 0.71, respectively. c Box-and-whisker plot of DNA methylation values in graft donors in T cell-replete HSCT (that is, without the application of in vivo alemtuzumab). In an independent sample cohort, we confirmed the observed DNA methylation phenotype, suggesting the epigenetic classifier is also effective in the context of a T cell-replete conditioning regimen ( P = 0.050). For two samples, C t -values could not be detected in the MethyLight experiments. d At a threshold of PMR = 17.73 (dotted line), the area under the ROC curve was 0.73 with a maximal specificity and sensitivity of 0.71 and 0.78, respectively

    Journal: Genome Medicine

    Article Title: A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

    doi: 10.1186/s13073-015-0246-z

    Figure Lengend Snippet: Validation of top-ranked DMP cg20475486 using a clinical biomarker assay. Replication of the top-ranked DMP associated with aGVHD severity, cg20475486, using a semi-quantitative DNA methylation assay. a Box-and-whisker plot of DNA methylation values in graft donors in T cell-depleted HSCT (initial discovery cohort). We replicated the DNA hypomethylation phenotype in HSCT donors matched to recipients with severe aGVHD compared to no/mild aGVHD ( P = 0.039, Wilcoxon rank-sum test). b At a relative DNA methylation threshold of 8.295 (dotted line), the AUC was 0.74 with a maximal specificity and sensitivity of 0.75 and 0.71, respectively. c Box-and-whisker plot of DNA methylation values in graft donors in T cell-replete HSCT (that is, without the application of in vivo alemtuzumab). In an independent sample cohort, we confirmed the observed DNA methylation phenotype, suggesting the epigenetic classifier is also effective in the context of a T cell-replete conditioning regimen ( P = 0.050). For two samples, C t -values could not be detected in the MethyLight experiments. d At a threshold of PMR = 17.73 (dotted line), the area under the ROC curve was 0.73 with a maximal specificity and sensitivity of 0.71 and 0.78, respectively

    Article Snippet: Measurement of relative DNA methylation levels using MethyLight Genomic DNA was bisulfite-converted using an EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions.

    Techniques: Biomarker Assay, DNA Methylation Assay, Whisker Assay, In Vivo

    Overview of the study design. We aimed to identify specific epigenetic marks in peripheral blood of healthy graft donors that delineate aGVHD severity in HLA-matched sibling recipients prior to HSCT. At the discovery stage, we assessed genome-wide DNA methylation levels in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, that is, ‘severe’ aGVHD (grades III + IV; n = 9) and ‘no/mild’ aGVHD (grades 0, I + II; n = 76). HSCT recipients received reduced-intensity (non-myeloablative) T cell-depleted conditioning using in vivo alemtuzumab. At the replication stage, we used a semi-quantitative DNA methylation assay, MethyLight, which can be easily used in a clinical setting. We validated the top-ranked differentially methylated positions associated with aGVHD severity status in donors in the context of both T cell-depleted and T cell-replete conditioning regimens for HSCT

    Journal: Genome Medicine

    Article Title: A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

    doi: 10.1186/s13073-015-0246-z

    Figure Lengend Snippet: Overview of the study design. We aimed to identify specific epigenetic marks in peripheral blood of healthy graft donors that delineate aGVHD severity in HLA-matched sibling recipients prior to HSCT. At the discovery stage, we assessed genome-wide DNA methylation levels in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, that is, ‘severe’ aGVHD (grades III + IV; n = 9) and ‘no/mild’ aGVHD (grades 0, I + II; n = 76). HSCT recipients received reduced-intensity (non-myeloablative) T cell-depleted conditioning using in vivo alemtuzumab. At the replication stage, we used a semi-quantitative DNA methylation assay, MethyLight, which can be easily used in a clinical setting. We validated the top-ranked differentially methylated positions associated with aGVHD severity status in donors in the context of both T cell-depleted and T cell-replete conditioning regimens for HSCT

    Article Snippet: Measurement of relative DNA methylation levels using MethyLight Genomic DNA was bisulfite-converted using an EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions.

    Techniques: Genome Wide, DNA Methylation Assay, In Vivo, Methylation

    EZH2 contributes to miR-454-3p downregulation via DNA methylation to promote polarization of M2 macrophages. (A) The expression of miR-454-3p in clinical samples of different grades of glioma detected by RT-PCR. * p

    Journal: Frontiers in Cell and Developmental Biology

    Article Title: EZH2-Inhibited MicroRNA-454-3p Promotes M2 Macrophage Polarization in Glioma

    doi: 10.3389/fcell.2020.574940

    Figure Lengend Snippet: EZH2 contributes to miR-454-3p downregulation via DNA methylation to promote polarization of M2 macrophages. (A) The expression of miR-454-3p in clinical samples of different grades of glioma detected by RT-PCR. * p

    Article Snippet: MS-PCR was then conducted with the DNA Methylation-GoldTM kit (D5005, Zymo Research, Irvine, CA, United States).

    Techniques: DNA Methylation Assay, Expressing, Reverse Transcription Polymerase Chain Reaction