dde i Takara Search Results


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  • 90
    Thermo Fisher veriti 96 well thermal cycler
    Veriti 96 Well Thermal Cycler, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 3546 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa dde i
    Schematic representation of primer design for detection of PML-RAR α mRNA by <t>RT-LAMP</t> and cutting sites of <t>Dde</t> I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.
    Dde I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dde  (Promega)
    88
    Promega dde
    RFLP of the <t>vanRSHAX</t> region digested with <t>Dde</t> I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).
    Dde, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa hinf i
    RFLP of the <t>vanRSHAX</t> region digested with <t>Dde</t> I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).
    Hinf I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa xsp i
    RFLP of the <t>vanRSHAX</t> region digested with <t>Dde</t> I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).
    Xsp I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa xho i
    RFLP of the <t>vanRSHAX</t> region digested with <t>Dde</t> I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).
    Xho I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 2825 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa cla i
    RFLP analysis of Tn 1546 -like elements amplified by <t>L-PCR</t> and digested with Cla I. For E. faecium 1641 and E. faecalis 7946 the L-PCR products were repeatedly obtained with a low efficiency; therefore, these samples were processed separately. M1 (λ/ Bst EII) and M2 (λ/ Hin dIII) are DNA molecular weight standards (Kucharczyk TE, Warsaw, Poland).
    Cla I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 84 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa dnase i
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Dnase I, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 8161 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    TaKaRa takara k buffer
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Takara K Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa k buffer
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    K Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher eco ri
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Eco Ri, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7256 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs taq i
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 388 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Toyobo quick taq hs dyemix
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Quick Taq Hs Dyemix, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 341 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eiken Chemical rt 160c loopamp realtime turbidimeter
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Rt 160c Loopamp Realtime Turbidimeter, supplied by Eiken Chemical, used in various techniques. Bioz Stars score: 96/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Toyobo primer
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Primer, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 354 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Toyobo polymerase chain reaction pcr
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Polymerase Chain Reaction Pcr, supplied by Toyobo, used in various techniques. Bioz Stars score: 99/100, based on 90 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eiken Chemical real time turbidity monitoring
    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of <t>DNase</t> I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.
    Real Time Turbidity Monitoring, supplied by Eiken Chemical, used in various techniques. Bioz Stars score: 94/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Schematic representation of primer design for detection of PML-RAR α mRNA by RT-LAMP and cutting sites of Dde I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Journal: Yonago Acta Medica

    Article Title: Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia–Retinoic Acid Receptor α mRNA

    doi:

    Figure Lengend Snippet: Schematic representation of primer design for detection of PML-RAR α mRNA by RT-LAMP and cutting sites of Dde I restriction enzyme assay. Exon numbers of the PML gene (dark) and the RAR α gene (light) are shown. PML , promyelocytic leukemia ; RAR α, retinoic acid receptor α; RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Article Snippet: The specificity of LAMP was confirmed by restriction enzyme digestion using Dde I (Takara Bio, Otsu, Japan) under the following conditions: 5 μL LAMP product was mixed with 2 μL of 10 × K buffer (Takara Bio), 1 μL Dde I, with distilled water added to obtain a final volume of 20 μL, followed by incubation at 37 °C for 120 min. Dde I was inactivated at 70 °C for 15 min and the digestion products (10-μL aliquots) were mixed with loading buffer (Nippon Gene, Toyama, Japan) and separated by 1.5% agarose gel electrophoresis (100 V, 35 min) with 0.005% ethidium bromide using a Mupid mini gel electrophoresis system (Advance, Tokyo, Japan), with 5 μL Gene Ladder 100 (Nippon Gene) used as a molecular size marker.

    Techniques: Enzymatic Assay, Amplification

    Dde I restriction enzyme digestion of RT-LAMP products. Products of bcr1, bcr2, and bcr3 plasmid DNA amplification were incubated with (+) or without (−) Dde I at 37 °C for 120 min, followed by deactivation at 70 °C for 15 min and separation by 1.5% agarose gel electrophoresis (100 V, 35 min). The amounts of bcr1, bcr2 and bcr3 plasmid DNAs were 8.8, 7.8, and 8.0 × 10 6 copies/tube, respectively. The expected sizes of digested RT-LAMP products are the followings: 468 bp, about 234 bp (stem and loop structure) and 83 bp for bcr1; 232 bp, about 116 bp (stem and loop structure) and 83 bp for bcr2; and 139 bp and 121 bp (merged in Figure) for bcr3. DW, distilled water (negative control); M, 100-bp ladder size marker; neg RNA, IVS-0035 RNA (negative control); RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Journal: Yonago Acta Medica

    Article Title: Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Simple and Rapid Detection of Promyelocytic Leukemia–Retinoic Acid Receptor α mRNA

    doi:

    Figure Lengend Snippet: Dde I restriction enzyme digestion of RT-LAMP products. Products of bcr1, bcr2, and bcr3 plasmid DNA amplification were incubated with (+) or without (−) Dde I at 37 °C for 120 min, followed by deactivation at 70 °C for 15 min and separation by 1.5% agarose gel electrophoresis (100 V, 35 min). The amounts of bcr1, bcr2 and bcr3 plasmid DNAs were 8.8, 7.8, and 8.0 × 10 6 copies/tube, respectively. The expected sizes of digested RT-LAMP products are the followings: 468 bp, about 234 bp (stem and loop structure) and 83 bp for bcr1; 232 bp, about 116 bp (stem and loop structure) and 83 bp for bcr2; and 139 bp and 121 bp (merged in Figure) for bcr3. DW, distilled water (negative control); M, 100-bp ladder size marker; neg RNA, IVS-0035 RNA (negative control); RT-LAMP, reverse transcription loop-mediated isothermal amplification.

    Article Snippet: The specificity of LAMP was confirmed by restriction enzyme digestion using Dde I (Takara Bio, Otsu, Japan) under the following conditions: 5 μL LAMP product was mixed with 2 μL of 10 × K buffer (Takara Bio), 1 μL Dde I, with distilled water added to obtain a final volume of 20 μL, followed by incubation at 37 °C for 120 min. Dde I was inactivated at 70 °C for 15 min and the digestion products (10-μL aliquots) were mixed with loading buffer (Nippon Gene, Toyama, Japan) and separated by 1.5% agarose gel electrophoresis (100 V, 35 min) with 0.005% ethidium bromide using a Mupid mini gel electrophoresis system (Advance, Tokyo, Japan), with 5 μL Gene Ladder 100 (Nippon Gene) used as a molecular size marker.

    Techniques: Plasmid Preparation, Amplification, Incubation, Agarose Gel Electrophoresis, Negative Control, Marker

    RFLP of the vanRSHAX region digested with Dde I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).

    Journal: Journal of Clinical Microbiology

    Article Title: Outbreak of Vancomycin-Resistant Enterococci in a Hospital in Gda?sk, Poland, due to Horizontal Transfer of Different Tn1546-Like Transposon Variants and Clonal Spread of Several Strains

    doi:

    Figure Lengend Snippet: RFLP of the vanRSHAX region digested with Dde I. The arrow indicates the DNA band of reduced mobility common for all the HW and ICU isolates. M1 (λ/ Bst EII) and M2 (pBR322/ Msp I) are DNA molecular weight standards (Kucharczyk TE).

    Article Snippet: The vanRSHAX amplicons were cut with the Dde I restrictase (Promega, Madison, Wis.) ( ) and electrophoresed in 2% agarose gels (SeaKem).

    Techniques: Molecular Weight

    RFLP analysis of Tn 1546 -like elements amplified by L-PCR and digested with Cla I. For E. faecium 1641 and E. faecalis 7946 the L-PCR products were repeatedly obtained with a low efficiency; therefore, these samples were processed separately. M1 (λ/ Bst EII) and M2 (λ/ Hin dIII) are DNA molecular weight standards (Kucharczyk TE, Warsaw, Poland).

    Journal: Journal of Clinical Microbiology

    Article Title: Outbreak of Vancomycin-Resistant Enterococci in a Hospital in Gda?sk, Poland, due to Horizontal Transfer of Different Tn1546-Like Transposon Variants and Clonal Spread of Several Strains

    doi:

    Figure Lengend Snippet: RFLP analysis of Tn 1546 -like elements amplified by L-PCR and digested with Cla I. For E. faecium 1641 and E. faecalis 7946 the L-PCR products were repeatedly obtained with a low efficiency; therefore, these samples were processed separately. M1 (λ/ Bst EII) and M2 (λ/ Hin dIII) are DNA molecular weight standards (Kucharczyk TE, Warsaw, Poland).

    Article Snippet: The L-PCR products containing Tn 1546 -like elements were digested independently with Cla I (Takara) ( ) and Eco RI (MBI Fermentas, Vilnius, Lithuania) restriction enzymes, and the resulting DNA fragments were separated in 1% agarose gels (SeaKem).

    Techniques: Amplification, Polymerase Chain Reaction, Molecular Weight

    Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of DNase I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.

    Journal: Nucleic Acids Research

    Article Title: NF-kappaB P50/P65 hetero-dimer mediates differential regulation of CD166/ALCAM expression via interaction with micoRNA-9 after serum deprivation, providing evidence for a novel negative auto-regulatory loop

    doi: 10.1093/nar/gkr302

    Figure Lengend Snippet: Binding of NF-κB to the CD166 promoter. ( A ) Schematic representation of the restriction enzyme positions and primers used to map the serum starvation-response site from −1190 to −465 (relative to the TSS) region by chart-PCR assays. ( B ) Nuclei of HepG2 cells before or after SD for 1 day were purified and digested with 5–15 U of different restriction enzymes, as indicated, per 100 μl reaction system for 30 min. Purified DNA treated with or without enzymes (uncut) was semi-quantitated using primer sets a–F and R after 30 cycles of PCR reactions. ( C ) Purified DNA from HepG2 cells before or after SD for 1 day treated with (cut) or without (uncut) 3 U of DNase I for 5 min at 37°C was semi-quantitated using primer sets R and a–e, which were the same as indicated in Figure 3 A after 29 PCR cycles. ( D ) Nuclear extracts from three different hepatoma cell lines treated with SD for 1 day were assayed by EMSA using biotin-labeled oligonucleotide probes (from −858 to −834) and NF-κB consensus probes. Shifted bands were verified by addition 5 μg either nonspecific control IgG or specific antibodies against P65 or P50, as indicated. ( E ) EMSA assays were performed using nuclear extracts from cells by treatment of SD for indicated time and wild-type probes (from −858 to −834). ( F ) ChIP analysis was performed to qualitatively confirm the interaction of NF-κB components, Pol II and Brg I with the promoter in vivo . As the negative controls, the protein–DNA complexes were incubated without antibodies or with non-specific control IgG. The input DNA represents 1/20th of the starting material. ( G ) In vivo interactions of NF-κB with CD166 promoter after SD upon suppression of P50/P65 protein by specific siRNA were determined by ChIP assay.

    Article Snippet: Chromatin accessibility analysis Accessibility of DNA to digestion with DNase I or restriction enzymes (all from Takara, except Dde I and Mae III from New England Biolabs, Beverly, MA, USA) analyzed using chromatin accessibility by real-time PCR (CHART-PCR) as described previously ( ).

    Techniques: Binding Assay, Polymerase Chain Reaction, Purification, Labeling, Chromatin Immunoprecipitation, In Vivo, Incubation