fspei  (New England Biolabs)


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  • 95
    Name:
    FspEI
    Description:
    FspEI 200 units
    Catalog Number:
    r0662s
    Price:
    110
    Size:
    200 units
    Category:
    Restriction Enzymes
    Buy from Supplier


    Structured Review

    New England Biolabs fspei
    FspEI
    FspEI 200 units
    https://www.bioz.com/result/fspei/product/New England Biolabs
    Average 95 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    fspei - by Bioz Stars, 2020-09
    95/100 stars

    Images

    1) Product Images from "Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI"

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

    Journal: Genome Research

    doi: 10.1101/gr.222885.117

    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).
    Figure Legend Snippet: MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Techniques Used: Ligation, Fractionation, Amplification, Sequencing

    2) Product Images from "MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes"

    Article Title: MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes

    Journal: Open Biology

    doi: 10.1098/rsob.150130

    Schematic overview of the procedure for MethylRAD library preparation. Genomic DNA is digested with the restriction enzyme FspEI, producing 32-bp fragments including four-base 3′ overhangs. Adaptors with compatible overhangs (NNNN) are ligated to each end of these fragments. Tag density can be adjusted using adaptors with selective overhangs (e.g. NNNG). The constructs are amplified and purified by gel extraction. Sample-specific barcodes are incorporated in each construct by PCR, and the products pooled for sequencing.
    Figure Legend Snippet: Schematic overview of the procedure for MethylRAD library preparation. Genomic DNA is digested with the restriction enzyme FspEI, producing 32-bp fragments including four-base 3′ overhangs. Adaptors with compatible overhangs (NNNN) are ligated to each end of these fragments. Tag density can be adjusted using adaptors with selective overhangs (e.g. NNNG). The constructs are amplified and purified by gel extraction. Sample-specific barcodes are incorporated in each construct by PCR, and the products pooled for sequencing.

    Techniques Used: Construct, Amplification, Purification, Gel Extraction, Polymerase Chain Reaction, Sequencing

    3) Product Images from "Novel features of telomere biology revealed by the absence of telomeric DNA methylation"

    Article Title: Novel features of telomere biology revealed by the absence of telomeric DNA methylation

    Journal: Genome Research

    doi: 10.1101/gr.202465.115

    Methylation-dependent restriction enzyme analyses confirm the absence of telomeric DNA methylation. ( A ) Cartoon representing the sequence specificity of the restriction enzymes used to digest Arabidopsis genomic DNA. ( B ) Southern blot hybridizations of Arabidopsis genomic DNA digested with the restriction enzymes indicated in A . The upper panel shows equal amounts of undigested (Control) or digested (HpaII, FspEI, or McrBC) DNA samples hybridized with a telomeric probe. The four DNA samples were also digested with Tru9I prior to hybridization. The middle panel shows the hybridization of the same samples with a 180-bp centromeric repeat probe. The ethidium bromide staining of the samples is shown in the lower panel. The control DNA sample was run in the same gel as the rest of the samples, so that their corresponding hybridization signals were processed equally. ( C ) Bar plot representation of the telomeric and centromeric bottom band hybridization signals expressed as percentages of the control. C, H, F, and M represent Control, HpaII, FspEI, and McrBC, respectively.
    Figure Legend Snippet: Methylation-dependent restriction enzyme analyses confirm the absence of telomeric DNA methylation. ( A ) Cartoon representing the sequence specificity of the restriction enzymes used to digest Arabidopsis genomic DNA. ( B ) Southern blot hybridizations of Arabidopsis genomic DNA digested with the restriction enzymes indicated in A . The upper panel shows equal amounts of undigested (Control) or digested (HpaII, FspEI, or McrBC) DNA samples hybridized with a telomeric probe. The four DNA samples were also digested with Tru9I prior to hybridization. The middle panel shows the hybridization of the same samples with a 180-bp centromeric repeat probe. The ethidium bromide staining of the samples is shown in the lower panel. The control DNA sample was run in the same gel as the rest of the samples, so that their corresponding hybridization signals were processed equally. ( C ) Bar plot representation of the telomeric and centromeric bottom band hybridization signals expressed as percentages of the control. C, H, F, and M represent Control, HpaII, FspEI, and McrBC, respectively.

    Techniques Used: Methylation, DNA Methylation Assay, Sequencing, Southern Blot, Hybridization, Staining

    Related Articles

    Sequencing:

    Article Title: MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes
    Article Snippet: .. MethylRAD library preparation and sequencing MethylRAD library preparation began with digestion of 1–200 ng genomic DNA in a 15 µl reaction containing 4 U FspEI (NEB) at 37°C for 4 h. Five µl of the digested product was run on a 1% agarose gel to verify digestion. .. Then, 10 µl ligation master mix containing 0.2 µM each of two adaptors, 1 mM ATP and 800 U of T4 DNA ligase (NEB) was added to the digestion solution, and incubated for 6–12 h at 4°C.

    Article Title: DNA methylation analysis in malignant pheochromocytoma and paraganglioma
    Article Snippet: .. In this study, we employed two types of methylation-dependent restriction enzymes: MspJI (New England Biolabs, Beverly, MA, USA), which cleaves DNA 9 bp downstream from the m CNNR (N = A, T, G or C; R = G or C) sequence , , and FspEI (New England Biolabs), which cleaves DNA 12 bp downstream from the Cm C sequence . .. One microgram of the extracted DNA was incubated with 4 units of the appropriate two enzymes at 37 °C for 8 h in 30 μl of readymade reaction buffer (New England Biolabs) .

    other:

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
    Article Snippet: LpnPI, FspEI, and MspJI (New England Biolabs) digestions were carried out according to the manufacturer's protocol.

    Agarose Gel Electrophoresis:

    Article Title: MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes
    Article Snippet: .. MethylRAD library preparation and sequencing MethylRAD library preparation began with digestion of 1–200 ng genomic DNA in a 15 µl reaction containing 4 U FspEI (NEB) at 37°C for 4 h. Five µl of the digested product was run on a 1% agarose gel to verify digestion. .. Then, 10 µl ligation master mix containing 0.2 µM each of two adaptors, 1 mM ATP and 800 U of T4 DNA ligase (NEB) was added to the digestion solution, and incubated for 6–12 h at 4°C.

    Infection:

    Article Title: Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples
    Article Snippet: .. One hundred twenty-five to 500 ng of gDNA extracted from P. vivax -infected whole-blood samples was digested with 5 units of FspEI (New England Biolabs) and 5 units of MspJI (New England Biolabs) enzymes in a 30-µl reaction mixture. ..

    Methylation:

    Article Title: DNA methylation analysis in malignant pheochromocytoma and paraganglioma
    Article Snippet: .. In this study, we employed two types of methylation-dependent restriction enzymes: MspJI (New England Biolabs, Beverly, MA, USA), which cleaves DNA 9 bp downstream from the m CNNR (N = A, T, G or C; R = G or C) sequence , , and FspEI (New England Biolabs), which cleaves DNA 12 bp downstream from the Cm C sequence . .. One microgram of the extracted DNA was incubated with 4 units of the appropriate two enzymes at 37 °C for 8 h in 30 μl of readymade reaction buffer (New England Biolabs) .

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  • 95
    New England Biolabs fspei
    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with <t>LpnPI,</t> followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and <t>FspEI</t> CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).
    Fspei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fspei/product/New England Biolabs
    Average 95 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    fspei - by Bioz Stars, 2020-09
    95/100 stars
      Buy from Supplier

    Image Search Results


    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Journal: Genome Research

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

    doi: 10.1101/gr.222885.117

    Figure Lengend Snippet: MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Article Snippet: LpnPI, FspEI, and MspJI (New England Biolabs) digestions were carried out according to the manufacturer's protocol.

    Techniques: Ligation, Fractionation, Amplification, Sequencing

    Schematic overview of the procedure for MethylRAD library preparation. Genomic DNA is digested with the restriction enzyme FspEI, producing 32-bp fragments including four-base 3′ overhangs. Adaptors with compatible overhangs (NNNN) are ligated to each end of these fragments. Tag density can be adjusted using adaptors with selective overhangs (e.g. NNNG). The constructs are amplified and purified by gel extraction. Sample-specific barcodes are incorporated in each construct by PCR, and the products pooled for sequencing.

    Journal: Open Biology

    Article Title: MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes

    doi: 10.1098/rsob.150130

    Figure Lengend Snippet: Schematic overview of the procedure for MethylRAD library preparation. Genomic DNA is digested with the restriction enzyme FspEI, producing 32-bp fragments including four-base 3′ overhangs. Adaptors with compatible overhangs (NNNN) are ligated to each end of these fragments. Tag density can be adjusted using adaptors with selective overhangs (e.g. NNNG). The constructs are amplified and purified by gel extraction. Sample-specific barcodes are incorporated in each construct by PCR, and the products pooled for sequencing.

    Article Snippet: MethylRAD library preparation and sequencing MethylRAD library preparation began with digestion of 1–200 ng genomic DNA in a 15 µl reaction containing 4 U FspEI (NEB) at 37°C for 4 h. Five µl of the digested product was run on a 1% agarose gel to verify digestion.

    Techniques: Construct, Amplification, Purification, Gel Extraction, Polymerase Chain Reaction, Sequencing

    Methylation-dependent restriction enzyme analyses confirm the absence of telomeric DNA methylation. ( A ) Cartoon representing the sequence specificity of the restriction enzymes used to digest Arabidopsis genomic DNA. ( B ) Southern blot hybridizations of Arabidopsis genomic DNA digested with the restriction enzymes indicated in A . The upper panel shows equal amounts of undigested (Control) or digested (HpaII, FspEI, or McrBC) DNA samples hybridized with a telomeric probe. The four DNA samples were also digested with Tru9I prior to hybridization. The middle panel shows the hybridization of the same samples with a 180-bp centromeric repeat probe. The ethidium bromide staining of the samples is shown in the lower panel. The control DNA sample was run in the same gel as the rest of the samples, so that their corresponding hybridization signals were processed equally. ( C ) Bar plot representation of the telomeric and centromeric bottom band hybridization signals expressed as percentages of the control. C, H, F, and M represent Control, HpaII, FspEI, and McrBC, respectively.

    Journal: Genome Research

    Article Title: Novel features of telomere biology revealed by the absence of telomeric DNA methylation

    doi: 10.1101/gr.202465.115

    Figure Lengend Snippet: Methylation-dependent restriction enzyme analyses confirm the absence of telomeric DNA methylation. ( A ) Cartoon representing the sequence specificity of the restriction enzymes used to digest Arabidopsis genomic DNA. ( B ) Southern blot hybridizations of Arabidopsis genomic DNA digested with the restriction enzymes indicated in A . The upper panel shows equal amounts of undigested (Control) or digested (HpaII, FspEI, or McrBC) DNA samples hybridized with a telomeric probe. The four DNA samples were also digested with Tru9I prior to hybridization. The middle panel shows the hybridization of the same samples with a 180-bp centromeric repeat probe. The ethidium bromide staining of the samples is shown in the lower panel. The control DNA sample was run in the same gel as the rest of the samples, so that their corresponding hybridization signals were processed equally. ( C ) Bar plot representation of the telomeric and centromeric bottom band hybridization signals expressed as percentages of the control. C, H, F, and M represent Control, HpaII, FspEI, and McrBC, respectively.

    Article Snippet: Equal amounts of genomic DNA (500 ng) were undigested or digested with the restriction enzymes HpaII, FspEI, or McrBC following the supplier's instructions (New England Biolabs).

    Techniques: Methylation, DNA Methylation Assay, Sequencing, Southern Blot, Hybridization, Staining