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  • 99
    New England Biolabs msei
    CGI methylation and mRNA expression of ZIC2 in pediatric medulloblastoma. ( a ) Schematic presentation of the predicted ZIC2 CpG island in the 5' UTR of the gene (chr13: 99428130-99428406) delineated according to the criteria by Gardiner-Garden and Frommer ( 52 ). <t>MseI-sites</t> flanking the ends of the CGI clone are shown together with their position in relation to the transcription start site. Pyrosequencing was performed for the indicated region. ( b ) Comparison between pyrosequencing results (grey bars) and aPRIMES results (black bars). For comparison, aPRIMES ratios were linearized and are given in relation to the linear ratio of tumor M3 that displayed the highest ratio among all aPRIMES samples, and was therefore set to 100%. For the pyrosequencing data, a median over all 12 investigated individual CpG sites was calculated. The right panel illustrates non-normalized spot-data after performance of aRPIMES. Triplicate spots for both ZIC2 clones, namely CGI-027A11 and CGI-028A11 are indicated Fem. (male) pool = <t>DNA</t> derived from the peripheral blood mononuclear cells (PBMCs) of 10 healthy donors below age 35. Cb pool = pool of cerebellum DNA from five unaffected donors, age 25–33 years. M1–M20: pediatric medulloblastoma samples. For medulloblastoma M8 no chip data are available. ( c ) mRNA abundance of ZIC2 was assessed by quantitative real-time PCR and normalized to the expression of ZIC2 in a cerebellum mRNA pool of 24 unaffected individuals. Medians and MADs of two independent experiments are shown. ZIC2 was downregulated to different degrees in all tested medulloblastomas, most profoundly in tumor M3 that displayed the highest methylation of the CGI.
    Msei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1422 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/msei/product/New England Biolabs
    Average 99 stars, based on 1422 article reviews
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    88
    Thermo Fisher tru1 i
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Tru1 I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 88 stars, based on 19 article reviews
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    92
    Thermo Fisher msei
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Msei, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 232 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    msei  (TaKaRa)
    93
    TaKaRa msei
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Msei, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Kaneka Corp msei adapter
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Msei Adapter, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Millipore msei primer
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Msei Primer, supplied by Millipore, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher msei adapters
    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, <t>Tru1</t> I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation
    Msei Adapters, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher msei adaptor pairs
    Digitized AFLP patterns of Bacillus taxa generated using primer sets <t>EcoRI</t> plus <t>C/MseI</t> plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for
    Msei Adaptor Pairs, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Genomed GmbH msei ca primer
    Digitized AFLP patterns of Bacillus taxa generated using primer sets <t>EcoRI</t> plus <t>C/MseI</t> plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for
    Msei Ca Primer, supplied by Genomed GmbH, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/msei ca primer/product/Genomed GmbH
    Average 92 stars, based on 8 article reviews
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    Image Search Results


    CGI methylation and mRNA expression of ZIC2 in pediatric medulloblastoma. ( a ) Schematic presentation of the predicted ZIC2 CpG island in the 5' UTR of the gene (chr13: 99428130-99428406) delineated according to the criteria by Gardiner-Garden and Frommer ( 52 ). MseI-sites flanking the ends of the CGI clone are shown together with their position in relation to the transcription start site. Pyrosequencing was performed for the indicated region. ( b ) Comparison between pyrosequencing results (grey bars) and aPRIMES results (black bars). For comparison, aPRIMES ratios were linearized and are given in relation to the linear ratio of tumor M3 that displayed the highest ratio among all aPRIMES samples, and was therefore set to 100%. For the pyrosequencing data, a median over all 12 investigated individual CpG sites was calculated. The right panel illustrates non-normalized spot-data after performance of aRPIMES. Triplicate spots for both ZIC2 clones, namely CGI-027A11 and CGI-028A11 are indicated Fem. (male) pool = DNA derived from the peripheral blood mononuclear cells (PBMCs) of 10 healthy donors below age 35. Cb pool = pool of cerebellum DNA from five unaffected donors, age 25–33 years. M1–M20: pediatric medulloblastoma samples. For medulloblastoma M8 no chip data are available. ( c ) mRNA abundance of ZIC2 was assessed by quantitative real-time PCR and normalized to the expression of ZIC2 in a cerebellum mRNA pool of 24 unaffected individuals. Medians and MADs of two independent experiments are shown. ZIC2 was downregulated to different degrees in all tested medulloblastomas, most profoundly in tumor M3 that displayed the highest methylation of the CGI.

    Journal: Nucleic Acids Research

    Article Title: Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma

    doi: 10.1093/nar/gkm094

    Figure Lengend Snippet: CGI methylation and mRNA expression of ZIC2 in pediatric medulloblastoma. ( a ) Schematic presentation of the predicted ZIC2 CpG island in the 5' UTR of the gene (chr13: 99428130-99428406) delineated according to the criteria by Gardiner-Garden and Frommer ( 52 ). MseI-sites flanking the ends of the CGI clone are shown together with their position in relation to the transcription start site. Pyrosequencing was performed for the indicated region. ( b ) Comparison between pyrosequencing results (grey bars) and aPRIMES results (black bars). For comparison, aPRIMES ratios were linearized and are given in relation to the linear ratio of tumor M3 that displayed the highest ratio among all aPRIMES samples, and was therefore set to 100%. For the pyrosequencing data, a median over all 12 investigated individual CpG sites was calculated. The right panel illustrates non-normalized spot-data after performance of aRPIMES. Triplicate spots for both ZIC2 clones, namely CGI-027A11 and CGI-028A11 are indicated Fem. (male) pool = DNA derived from the peripheral blood mononuclear cells (PBMCs) of 10 healthy donors below age 35. Cb pool = pool of cerebellum DNA from five unaffected donors, age 25–33 years. M1–M20: pediatric medulloblastoma samples. For medulloblastoma M8 no chip data are available. ( c ) mRNA abundance of ZIC2 was assessed by quantitative real-time PCR and normalized to the expression of ZIC2 in a cerebellum mRNA pool of 24 unaffected individuals. Medians and MADs of two independent experiments are shown. ZIC2 was downregulated to different degrees in all tested medulloblastomas, most profoundly in tumor M3 that displayed the highest methylation of the CGI.

    Article Snippet: aPRIMES Here, 500 ng genomic DNA was restricted to completion with 10 U MseI for 3 h in a final volume of 10 µl in the buffer provided by the supplier (New England Biolabs, Beverly, USA).

    Techniques: Methylation, Expressing, Clone Assay, Derivative Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Confirmation of SNP detected by the RESCAN type I approach . A. RESCAN type I SNP can be identified in sites that are found for the target restriction site in the query (in this case IR64) but are absent in the reference. In most cases, examination of the reference sequence reveals the presence of a proto sequence, i.e. a sequence that diverges by one base from the expected sequence TTAA: VTAA, TVAA, TTBA, TTAB, where V and B are, respectively, not T and not A. For a proto such as GTAA, a T > G SNP is inferred. A SNP cannot be inferred for a proto site such as TTTAG since either T3 > A or G5 > A could have produced the MseI site. B. We chose 20 type I sites that allowed inference and were detected through 1 or 2 RESCAN reads. The products amplified using flanking PCR primers from Nipponbare and IR64 are shown. C. The amplified products were subjected to digestion with MseI and analyzed by agarose gel electrophoresis. The presence of an extra restriction site in the amplified IR64 DNA and not in the control Nipponbare is evident in 17 of the 19 amplified products, confirming the presence of a SNP producing a restriction site in IR64.

    Journal: BMC Genomics

    Article Title: Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

    doi: 10.1186/1471-2164-13-72

    Figure Lengend Snippet: Confirmation of SNP detected by the RESCAN type I approach . A. RESCAN type I SNP can be identified in sites that are found for the target restriction site in the query (in this case IR64) but are absent in the reference. In most cases, examination of the reference sequence reveals the presence of a proto sequence, i.e. a sequence that diverges by one base from the expected sequence TTAA: VTAA, TVAA, TTBA, TTAB, where V and B are, respectively, not T and not A. For a proto such as GTAA, a T > G SNP is inferred. A SNP cannot be inferred for a proto site such as TTTAG since either T3 > A or G5 > A could have produced the MseI site. B. We chose 20 type I sites that allowed inference and were detected through 1 or 2 RESCAN reads. The products amplified using flanking PCR primers from Nipponbare and IR64 are shown. C. The amplified products were subjected to digestion with MseI and analyzed by agarose gel electrophoresis. The presence of an extra restriction site in the amplified IR64 DNA and not in the control Nipponbare is evident in 17 of the 19 amplified products, confirming the presence of a SNP producing a restriction site in IR64.

    Article Snippet: Method development Approximately 1000 ng of DNA was digested with the restriction enzyme MseI (T↓TAA, NEB, Ipswich, Massachusetts, cat. no. R0525) for 1 to 6 hour at 37°C.

    Techniques: Sequencing, Produced, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis

    Restriction enzyme analysis of influenza A H5 HA real-time RT-PCR amplicons. (a) MseI and Taq α I digestion of H5 WT (clade 1 and 2) and positive control (clade 3) HA amplicons. In the lane descriptions below, numbers in brackets after strain names

    Journal:

    Article Title: Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans ▿

    doi: 10.1128/JCM.02007-06

    Figure Lengend Snippet: Restriction enzyme analysis of influenza A H5 HA real-time RT-PCR amplicons. (a) MseI and Taq α I digestion of H5 WT (clade 1 and 2) and positive control (clade 3) HA amplicons. In the lane descriptions below, numbers in brackets after strain names

    Article Snippet: The sequence TCGA (nucleotides 840 to 844) observed in HA sequences of clade 1 and 2 H5 viruses, but absent in A/Duck/Singapore-Q/F119-3/1997, is recognized and cleaved by the restriction enzyme Taqα I. Fifteen microliters of the H5 TaqMan real-time RT-PCR mix containing the 151-bp PCR product amplified from the HA1 portion of the influenza A H5 HA was added to 0.5 μl of the restriction enzymes MseI (5 U) or Taqα I (10 U) (New England Biolabs, Beverly, MA) for a minimum of 60 min at 37°C or 60°C, respectively, in 50 mM NaCl-10 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for MseI digestion or 100 mM NaCl-50 mM Tris-HCl-10 mM MgCl2 -1 mM dithiothreitol-100 μg/ml bovine serum albumin [pH 7.9] for Taqα I digestion.

    Techniques: Quantitative RT-PCR, Positive Control

    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Journal: PLoS ONE

    Article Title: A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

    doi: 10.1371/journal.pone.0026775

    Figure Lengend Snippet: Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Article Snippet: Subsequently, proteins were inactivated by heating to 95°C for 10 min and the DNA probe was digested with Mse I (NEB).

    Techniques: In Vivo, Mutagenesis, Irradiation, In Vitro, Incubation

    Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, Tru1 I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation

    Journal:

    Article Title: Analysis of Carica papaya Telomeres and Telomere-Associated Proteins: Insights into the Evolution of Telomere Maintenance in Brassicales

    doi: 10.1007/s12042-008-9018-x

    Figure Lengend Snippet: Telomere length analysis in members of the Brassicales Order. a TRF analysis of papaya telomeres. Lane 1, Tru1 I digestion of genomic DNA without prior Bal 31 treatment (0 min), lanes 2–6, Tru1 I digestion of genomic DNA after various incubation

    Article Snippet: TRF analysis was performed with Tru1 I (Fermentas) restriction enzyme and 32 P 5′ end-labeled (T3 AG3 )4 oligonucleotide as a probe [ ].

    Techniques: Incubation

    Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for

    Journal: Applied and Environmental Microbiology

    Article Title: Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis

    doi: 10.1128/AEM.70.5.2786-2790.2004

    Figure Lengend Snippet: Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for

    Article Snippet: EcoRI and MseI adaptor pairs (Applied Biosystems) were ligated to restriction fragments according to the manufacturer's protocol.

    Techniques: Generated