u87mg dna  (New England Biolabs)


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    Name:
    Msp I Methyltransferase
    Description:
    Msp I Methyltransferase 100 units
    Catalog Number:
    m0215s
    Price:
    76
    Size:
    100 units
    Category:
    DNA Methylases
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    Structured Review

    New England Biolabs u87mg dna
    Msp I Methyltransferase
    Msp I Methyltransferase 100 units
    https://www.bioz.com/result/u87mg dna/product/New England Biolabs
    Average 91 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    u87mg dna - by Bioz Stars, 2020-10
    91/100 stars

    Images

    1) Product Images from "In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays"

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

    Journal: Frontiers in Neuroscience

    doi: 10.3389/neuro.15.005.2009

    Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.
    Figure Legend Snippet: Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.

    Techniques Used: Methylation Sequencing, Methylation

    BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.
    Figure Legend Snippet: BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.

    Techniques Used: Binding Assay, Methylation, Polymerase Chain Reaction, Methylation Sequencing, Amplification

    Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.
    Figure Legend Snippet: Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.

    Techniques Used: Methylation

    2) Product Images from "In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays"

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

    Journal: Frontiers in Neuroscience

    doi: 10.3389/neuro.15.005.2009

    Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.
    Figure Legend Snippet: Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.

    Techniques Used: Methylation Sequencing, Methylation

    BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.
    Figure Legend Snippet: BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.

    Techniques Used: Binding Assay, Methylation, Polymerase Chain Reaction, Methylation Sequencing, Amplification

    Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.
    Figure Legend Snippet: Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.

    Techniques Used: Methylation

    Related Articles

    Negative Control:

    Article Title: Phase II Study of Bevacizumab Plus Temozolomide During and After Radiation Therapy for Patients With Newly Diagnosed Glioblastoma Multiforme
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscataway, NJ), respectively. .. See accompanying editorial on page Supported in part by Genentech, American Brain Tumor Association/Mark Linder Small Project Grant, and Grant No. NIH/NCI K08CA124479 from the National Institutes of Health.

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively. .. Bisulfite sequencing validation Primers were designed with the assistance of the online tool MethPrimer (Li and Dahiya, ).

    Article Title: Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage
    Article Snippet: .. Samples were subjected to a two-stage nested PCR strategy using: first-stage primers (5′GGATAT GTTGGGATAGTT-3′ and 5′-CCAAAAACCCCAA ACCC-3′) and second-stage primers (unmethylated reaction: 5′-TTTGTGTTTTGATGTTTGTAGGTTTTTGT-3′ and 5′-AACTCCACACTCTTCCAAAAACAAAACA-3′; methylated reaction: 5′-TTTCGACGTTCGTAGGTTT TCGC-3′ and 5′-CACTCTTCCGAAAACGAAACG-3′).Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscat-away, NJ, USA). .. RT-PCR was performed using an Illustra Ready-to-Go RT-PCR kit (GE Healthcare, Little Chalfont, UK).

    Amplification:

    Article Title: Phase II Study of Bevacizumab Plus Temozolomide During and After Radiation Therapy for Patients With Newly Diagnosed Glioblastoma Multiforme
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscataway, NJ), respectively. .. See accompanying editorial on page Supported in part by Genentech, American Brain Tumor Association/Mark Linder Small Project Grant, and Grant No. NIH/NCI K08CA124479 from the National Institutes of Health.

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively. .. Bisulfite sequencing validation Primers were designed with the assistance of the online tool MethPrimer (Li and Dahiya, ).

    Article Title: Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage
    Article Snippet: .. Samples were subjected to a two-stage nested PCR strategy using: first-stage primers (5′GGATAT GTTGGGATAGTT-3′ and 5′-CCAAAAACCCCAA ACCC-3′) and second-stage primers (unmethylated reaction: 5′-TTTGTGTTTTGATGTTTGTAGGTTTTTGT-3′ and 5′-AACTCCACACTCTTCCAAAAACAAAACA-3′; methylated reaction: 5′-TTTCGACGTTCGTAGGTTT TCGC-3′ and 5′-CACTCTTCCGAAAACGAAACG-3′).Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscat-away, NJ, USA). .. RT-PCR was performed using an Illustra Ready-to-Go RT-PCR kit (GE Healthcare, Little Chalfont, UK).

    Whole Genome Amplification:

    Article Title: Phase II Study of Bevacizumab Plus Temozolomide During and After Radiation Therapy for Patients With Newly Diagnosed Glioblastoma Multiforme
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscataway, NJ), respectively. .. See accompanying editorial on page Supported in part by Genentech, American Brain Tumor Association/Mark Linder Small Project Grant, and Grant No. NIH/NCI K08CA124479 from the National Institutes of Health.

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays
    Article Snippet: .. Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively. .. Bisulfite sequencing validation Primers were designed with the assistance of the online tool MethPrimer (Li and Dahiya, ).

    Article Title: Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage
    Article Snippet: .. Samples were subjected to a two-stage nested PCR strategy using: first-stage primers (5′GGATAT GTTGGGATAGTT-3′ and 5′-CCAAAAACCCCAA ACCC-3′) and second-stage primers (unmethylated reaction: 5′-TTTGTGTTTTGATGTTTGTAGGTTTTTGT-3′ and 5′-AACTCCACACTCTTCCAAAAACAAAACA-3′; methylated reaction: 5′-TTTCGACGTTCGTAGGTTT TCGC-3′ and 5′-CACTCTTCCGAAAACGAAACG-3′).Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscat-away, NJ, USA). .. RT-PCR was performed using an Illustra Ready-to-Go RT-PCR kit (GE Healthcare, Little Chalfont, UK).

    Methylation:

    Article Title: Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose
    Article Snippet: .. DNA was methylated with MspI methyltransferase (NEB) for at least 4 h according to the manufacturer’s instructions. ..

    Article Title: Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage
    Article Snippet: .. Samples were subjected to a two-stage nested PCR strategy using: first-stage primers (5′GGATAT GTTGGGATAGTT-3′ and 5′-CCAAAAACCCCAA ACCC-3′) and second-stage primers (unmethylated reaction: 5′-TTTGTGTTTTGATGTTTGTAGGTTTTTGT-3′ and 5′-AACTCCACACTCTTCCAAAAACAAAACA-3′; methylated reaction: 5′-TTTCGACGTTCGTAGGTTT TCGC-3′ and 5′-CACTCTTCCGAAAACGAAACG-3′).Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscat-away, NJ, USA). .. RT-PCR was performed using an Illustra Ready-to-Go RT-PCR kit (GE Healthcare, Little Chalfont, UK).

    Purification:

    Article Title: Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations
    Article Snippet: .. The plasmid DNA was treated with MspI methyltransferase (New England Biolabs, Ipswich, MA) for 3 h, followed by purification with the DNA Clean and Concentrator Kit (Zymo Research, Irvine, CA). .. For each transformation, a 50-μl cell suspension was mixed with 2.0 μg of methylated plasmid DNA.

    Protein Purification:

    Article Title: The structure of SgrAI bound to DNA; recognition of an 8 base pair target
    Article Snippet: .. Protein purification SgrAI restriction endonuclease was expressed in Escherichia coli strain ER2566, from plasmid pET21a_SgrA1R, in the presence of the MspI methyltransferase expressed from the plasmid pBAKMspIM (New England Biolabs). ..

    Nested PCR:

    Article Title: Lyophilized brain tumor specimens can be used for histologic, nucleic acid, and protein analyses after 1 year of room temperature storage
    Article Snippet: .. Samples were subjected to a two-stage nested PCR strategy using: first-stage primers (5′GGATAT GTTGGGATAGTT-3′ and 5′-CCAAAAACCCCAA ACCC-3′) and second-stage primers (unmethylated reaction: 5′-TTTGTGTTTTGATGTTTGTAGGTTTTTGT-3′ and 5′-AACTCCACACTCTTCCAAAAACAAAACA-3′; methylated reaction: 5′-TTTCGACGTTCGTAGGTTT TCGC-3′ and 5′-CACTCTTCCGAAAACGAAACG-3′).Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (New England Biolabs, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, Piscat-away, NJ, USA). .. RT-PCR was performed using an Illustra Ready-to-Go RT-PCR kit (GE Healthcare, Little Chalfont, UK).

    Plasmid Preparation:

    Article Title: The structure of SgrAI bound to DNA; recognition of an 8 base pair target
    Article Snippet: .. Protein purification SgrAI restriction endonuclease was expressed in Escherichia coli strain ER2566, from plasmid pET21a_SgrA1R, in the presence of the MspI methyltransferase expressed from the plasmid pBAKMspIM (New England Biolabs). ..

    Article Title: Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations
    Article Snippet: .. The plasmid DNA was treated with MspI methyltransferase (New England Biolabs, Ipswich, MA) for 3 h, followed by purification with the DNA Clean and Concentrator Kit (Zymo Research, Irvine, CA). .. For each transformation, a 50-μl cell suspension was mixed with 2.0 μg of methylated plasmid DNA.

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    New England Biolabs u87mg dna
    Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, <t>U87MG</t> and GBM <t>DNA</t> samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.
    U87mg Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/u87mg dna/product/New England Biolabs
    Average 91 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    u87mg dna - by Bioz Stars, 2020-10
    91/100 stars
      Buy from Supplier

    Image Search Results


    Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.

    Journal: Frontiers in Neuroscience

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

    doi: 10.3389/neuro.15.005.2009

    Figure Lengend Snippet: Bisulfite sequencing validation results superimposed on MA plots . Bisulfite sequencing results (Table 2 ) were mapped on the corresponding MA plots for normal brain, U87MG and GBM DNA samples. Red dots represent validated methylated fragments (all CCGG sites are methylated in tandem), black dots represent fully unmethylated fragments, and blue dots represent mixed methylation of CCGG sites which are expected to be called unmethylated by MSRE. Light blue dots represent insensitive fragments, and light green dotes represent sensitive fragments. Light red highlighted sensitive fragments have M -values with p ≤ 0.001 and HpaII channel intensity with p ≤ 0.95. Also, the position of MGMT Fragment 2 (265 bp) has been indicated with a blue triangle.

    Article Snippet: Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively.

    Techniques: Methylation Sequencing, Methylation

    BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.

    Journal: Frontiers in Neuroscience

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

    doi: 10.3389/neuro.15.005.2009

    Figure Lengend Snippet: BfaI fragment coverage of the MGMT CpG island and bisulfite validation . (A) UCSC browser representation of MGMT CpG island showing two MSRE sensitive fragments in gray, predicted CpG island in blue, Agilent probes in green (note partial binding probes *), and methylation-specific PCR primers in red. Fragment 1 is 502 bp and contains 12 CCGG sites. Fragment 2 is 265 bp and contains 3 CCGG sites and binds MSP primers. Fragment 2 contains a portion of exon 1. (B) MSP results of human DNA samples confirm bisulfite sequencing with normal brain showing an unmethylated band, and GBM and U87MG showing a methylated band (as well as a unmethylated band). For controls, methylated SssI-treated DNA (pos.), and unmethylated whole genome amplified DNA (neg.) were analyzed in parallel. (C) Schematic diagram of bisulfite sequencing results on all CpG sites in Fragment 2 of uncloned GBM, U87MG, and normal DNA. Open circles indicate unmethylated CGs, and closed circles indicated methylated CGs. CGs in context of CCGG are enclosed in rectangles. Half-filled circles indicated sites where C peak (methylated) and T peak (unmethylated) from bisulfite sequencing were detected evenly.

    Article Snippet: Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively.

    Techniques: Binding Assay, Methylation, Polymerase Chain Reaction, Methylation Sequencing, Amplification

    Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.

    Journal: Frontiers in Neuroscience

    Article Title: In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

    doi: 10.3389/neuro.15.005.2009

    Figure Lengend Snippet: Comparison of methylation between U87MG, and GBM DNA samples . (A) Estimation of methylated fragments in all samples determined by using p ≤ 0.001 for each sample identifies 3,125 fragments (covering 2,417 CpG Islands). 4,414 fragments (3,321 CpG Islands) were common to both GBM and U87MG, 4,471 fragments (3,452 CpG Islands) common to both GBM and normal, and 3,518 fragments (2,704 CpG Islands) common to both normal and U87MG. (B) Estimation of uniquely methylated fragments using methylation determination based on p ≤ 0.001 and unmethylated determination based on p > 0.01. Fragments within the intermediate region with 0.001 ≤ p ≤ 0.01 are not categorized.

    Article Snippet: Positive and negative control samples for the MSP reaction were U87MG DNA treated with SssI methyltransferase (NEB, Ipswich, MA, USA) and whole-genome amplification of U87MG DNA using the GenomiPhi V2 Amplification kit (Amersham Biosciences, NJ, USA), respectively.

    Techniques: Methylation