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  • 99
    Agilent technologies brilliant iii sybr green qpcr master mix
    Sequence recognition by MAX/MGA is critical for recruiting PCGF6-PRC1 to its target genes. ( A ) MAX-dependent proliferation of ESCs. Schematic representation of FLAG-tagged wild type (WT) and mutant [L31V and E32D substitution (VD) and basic region deletion (Δb)] MAX proteins (left). Failure to rescue growth defects of Max -KO ESCs by either mutant MAX. Mock-transfected Max conditional KO ESCs (WT) stopped growing 4 days after doxycycline treatment (KO) (right). Stable expression of FLAG-tagged WT [KO+MAX(WT)] rescued the growth defect but VD or Δb mutants [KO+MAX(VD) and KO+MAX(Δb)] did not. ( B ) Association of mutant MAX proteins with other components of the PCGF6-PRC1 complex. Immunoprecipitation-immunoblot (IP-IB) analysis revealed the association of FLAG-tagged MAX WT, VD or Δb with HA-tagged PCGF6, RING1B and L3MBTL2. Max -KO ESCs that expressed HA-tagged PCGF6 and FLAG-tagged wild type or mutant MAX were subjected to IP with anti-FLAG antibody. Resulting precipitates (IP) and lysates (Input) were immunoblotted with antibodies against FLAG, HA, RING1B or L3MBTL2. ( C ) Binding of FLAG-tagged WT or mutant MAX to target of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least <t>three</t> independent experiments. ( D ) Binding of HA-tagged genes in Max -KO ESCs. Local levels of FLAG-tagged WT or mutant MAX at Ddx4 or Tdrd1 promoter regions were determined by <t>ChIP-qPCR.</t> The relative amount PCGF6 to target genes in Max -KO ESCs that express WT or mutant MAX. Local levels of HA-tagged PCGF6 at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. ( E ) Forced tethering of MAX to a TetO array induced activation of PCGF6-PRC1 recruitment. ChIP analysis for TetR, HA-tag (PCGF6), H2AK119ub1, H3K27me3, H3K27ac and H3 across the TetO-containing locus in ESCs revealed TetR-MAX-mediated local activation of the PCGF6-PRC1 pathway. ChIP experiments were performed at least in biological duplicate with error bars showing SEM. DOI: http://dx.doi.org/10.7554/eLife.21064.011
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    Agilent technologies briliant iii sybr green qpcr master mix
    Sequence recognition by MAX/MGA is critical for recruiting PCGF6-PRC1 to its target genes. ( A ) MAX-dependent proliferation of ESCs. Schematic representation of FLAG-tagged wild type (WT) and mutant [L31V and E32D substitution (VD) and basic region deletion (Δb)] MAX proteins (left). Failure to rescue growth defects of Max -KO ESCs by either mutant MAX. Mock-transfected Max conditional KO ESCs (WT) stopped growing 4 days after doxycycline treatment (KO) (right). Stable expression of FLAG-tagged WT [KO+MAX(WT)] rescued the growth defect but VD or Δb mutants [KO+MAX(VD) and KO+MAX(Δb)] did not. ( B ) Association of mutant MAX proteins with other components of the PCGF6-PRC1 complex. Immunoprecipitation-immunoblot (IP-IB) analysis revealed the association of FLAG-tagged MAX WT, VD or Δb with HA-tagged PCGF6, RING1B and L3MBTL2. Max -KO ESCs that expressed HA-tagged PCGF6 and FLAG-tagged wild type or mutant MAX were subjected to IP with anti-FLAG antibody. Resulting precipitates (IP) and lysates (Input) were immunoblotted with antibodies against FLAG, HA, RING1B or L3MBTL2. ( C ) Binding of FLAG-tagged WT or mutant MAX to target of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least <t>three</t> independent experiments. ( D ) Binding of HA-tagged genes in Max -KO ESCs. Local levels of FLAG-tagged WT or mutant MAX at Ddx4 or Tdrd1 promoter regions were determined by <t>ChIP-qPCR.</t> The relative amount PCGF6 to target genes in Max -KO ESCs that express WT or mutant MAX. Local levels of HA-tagged PCGF6 at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. ( E ) Forced tethering of MAX to a TetO array induced activation of PCGF6-PRC1 recruitment. ChIP analysis for TetR, HA-tag (PCGF6), H2AK119ub1, H3K27me3, H3K27ac and H3 across the TetO-containing locus in ESCs revealed TetR-MAX-mediated local activation of the PCGF6-PRC1 pathway. ChIP experiments were performed at least in biological duplicate with error bars showing SEM. DOI: http://dx.doi.org/10.7554/eLife.21064.011
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    Agilent technologies brilliant iii ultra fast qpcr master mix
    MiR-specific <t>qPCR</t> on synthetic templates with DNA primers . A The effect of primer concentration on Cq value of ssc-let-7d and ssc-miR-26a miR-specific qPCR assays. Real-time PCR assays were performed in parallel at <t>three</t> different concentrations (125, 250 and 500 nM) of the forward and of the reverse primers. B Amplification curves of an eight log 10 dilution series of a synthetic ssc-let-7d template in the ssc-let-7d miR-specific qPCR assays. All samples contained a final concentration of 0.2 ng/μl salmon sperm DNA. C Extrapolation of Cq as function of the log 10 of the number of templates for the same experiment as in B was a straight line (R 2 = 0.9993) with slope of -3.341 (PCR efficiency = 99%) over eight log 10 dilution of the template. D Melting curve analysis of the same experiment. No template control is labeled ntc. Melting curve analysis was performed from 60°C to 99°C.
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    Agilent technologies brilliant iii sybr green ultrafast qpcr master mix
    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of <t>three</t> independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time <t>qPCR</t> analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.
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    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of <t>three</t> independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time <t>qPCR</t> analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.
    Brillant Iii Ultrafast Sybr Green Qpcr Master Mix, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies brilliant iii qpcr master mix
    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of <t>three</t> independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time <t>qPCR</t> analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.
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    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of <t>three</t> independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time <t>qPCR</t> analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.
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    Agilent technologies brillliant iii ultra fast sybr green qpcr master mix
    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of <t>three</t> independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time <t>qPCR</t> analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.
    Brillliant Iii Ultra Fast Sybr Green Qpcr Master Mix, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 87/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Brilliant Iii Ultra Fast Sybr Green Qpcr Master Mix Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 98/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Brillant Iii Ultra Fast Sybr Green Qpcr Master Mix Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 77/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
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    Agilent technologies brilliant iii sybr green qpcr master mix plus rox reference dye
    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Brilliant Iii Sybr Green Qpcr Master Mix Plus Rox Reference Dye, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 78/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Brilliant Iii Ultra Fast Sybr Green Qpcr Master Mix Solution, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 78/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Brilliant Iii Sybr Green Qpcr Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
    Real Time Pcr Brilliant Iii Ultra Fast Sybr Green Qpcr Master Mix, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
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    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of <t>three</t> experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using <t>RT-qPCR</t> as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.
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    mCMV-infected Siglec-H KO mice exhibit a strong up-regulation of type-I IFN response genes 26 wk after infection. (A) RNA from splenic cells of mCMV-infected WT (wt) or Siglec-H KO (ko) mice and noninfected controls were isolated, and mRNA expression of different type I IFN–inducible genes was measured by <t>qRT-PCR</t> relative to mCMV-infected WT mice, whose expression levels were set to 1. Actin served as a housekeeping gene. Relative mRNA levels of IRF7 and CXCL10 10 wk after mCMV infection and 26 wk after mCMV infection are shown. Data are representative of two independent experiments ( n = 6 for each experiment). **, P
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    Image Search Results


    Sequence recognition by MAX/MGA is critical for recruiting PCGF6-PRC1 to its target genes. ( A ) MAX-dependent proliferation of ESCs. Schematic representation of FLAG-tagged wild type (WT) and mutant [L31V and E32D substitution (VD) and basic region deletion (Δb)] MAX proteins (left). Failure to rescue growth defects of Max -KO ESCs by either mutant MAX. Mock-transfected Max conditional KO ESCs (WT) stopped growing 4 days after doxycycline treatment (KO) (right). Stable expression of FLAG-tagged WT [KO+MAX(WT)] rescued the growth defect but VD or Δb mutants [KO+MAX(VD) and KO+MAX(Δb)] did not. ( B ) Association of mutant MAX proteins with other components of the PCGF6-PRC1 complex. Immunoprecipitation-immunoblot (IP-IB) analysis revealed the association of FLAG-tagged MAX WT, VD or Δb with HA-tagged PCGF6, RING1B and L3MBTL2. Max -KO ESCs that expressed HA-tagged PCGF6 and FLAG-tagged wild type or mutant MAX were subjected to IP with anti-FLAG antibody. Resulting precipitates (IP) and lysates (Input) were immunoblotted with antibodies against FLAG, HA, RING1B or L3MBTL2. ( C ) Binding of FLAG-tagged WT or mutant MAX to target of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least three independent experiments. ( D ) Binding of HA-tagged genes in Max -KO ESCs. Local levels of FLAG-tagged WT or mutant MAX at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. The relative amount PCGF6 to target genes in Max -KO ESCs that express WT or mutant MAX. Local levels of HA-tagged PCGF6 at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. ( E ) Forced tethering of MAX to a TetO array induced activation of PCGF6-PRC1 recruitment. ChIP analysis for TetR, HA-tag (PCGF6), H2AK119ub1, H3K27me3, H3K27ac and H3 across the TetO-containing locus in ESCs revealed TetR-MAX-mediated local activation of the PCGF6-PRC1 pathway. ChIP experiments were performed at least in biological duplicate with error bars showing SEM. DOI: http://dx.doi.org/10.7554/eLife.21064.011

    Journal: eLife

    Article Title: PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes

    doi: 10.7554/eLife.21064

    Figure Lengend Snippet: Sequence recognition by MAX/MGA is critical for recruiting PCGF6-PRC1 to its target genes. ( A ) MAX-dependent proliferation of ESCs. Schematic representation of FLAG-tagged wild type (WT) and mutant [L31V and E32D substitution (VD) and basic region deletion (Δb)] MAX proteins (left). Failure to rescue growth defects of Max -KO ESCs by either mutant MAX. Mock-transfected Max conditional KO ESCs (WT) stopped growing 4 days after doxycycline treatment (KO) (right). Stable expression of FLAG-tagged WT [KO+MAX(WT)] rescued the growth defect but VD or Δb mutants [KO+MAX(VD) and KO+MAX(Δb)] did not. ( B ) Association of mutant MAX proteins with other components of the PCGF6-PRC1 complex. Immunoprecipitation-immunoblot (IP-IB) analysis revealed the association of FLAG-tagged MAX WT, VD or Δb with HA-tagged PCGF6, RING1B and L3MBTL2. Max -KO ESCs that expressed HA-tagged PCGF6 and FLAG-tagged wild type or mutant MAX were subjected to IP with anti-FLAG antibody. Resulting precipitates (IP) and lysates (Input) were immunoblotted with antibodies against FLAG, HA, RING1B or L3MBTL2. ( C ) Binding of FLAG-tagged WT or mutant MAX to target of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least three independent experiments. ( D ) Binding of HA-tagged genes in Max -KO ESCs. Local levels of FLAG-tagged WT or mutant MAX at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. The relative amount PCGF6 to target genes in Max -KO ESCs that express WT or mutant MAX. Local levels of HA-tagged PCGF6 at Ddx4 or Tdrd1 promoter regions were determined by ChIP-qPCR. ( E ) Forced tethering of MAX to a TetO array induced activation of PCGF6-PRC1 recruitment. ChIP analysis for TetR, HA-tag (PCGF6), H2AK119ub1, H3K27me3, H3K27ac and H3 across the TetO-containing locus in ESCs revealed TetR-MAX-mediated local activation of the PCGF6-PRC1 pathway. ChIP experiments were performed at least in biological duplicate with error bars showing SEM. DOI: http://dx.doi.org/10.7554/eLife.21064.011

    Article Snippet: Real-time qPCR was performed using the Brilliant III SYBR Green QPCR Master Mix (Agilent).

    Techniques: Sequencing, Mutagenesis, Transfection, Expressing, Immunoprecipitation, Binding Assay, Standard Deviation, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Activation Assay

    The role of MAX/MGA in recruiting PCGF6-PRC1 to its target genes. ( A ) The expression of FLAG-tagged exogenous PCGF6 in wild type (WT) and Eed -KO ESCs. Expression levels of FLAG-tagged PCGF6 and endogenous LAMIN B protein in wild type and Eed -KO ESCs mock or FLAG-PCGF6 construct transfected were tested by immunoblotting. ( B ) Local levels of FLAG at the indicated promoter regions in wild type or Eed -KO ESCs expressing FLAG-tagged PCGF6 were determined by ChIP-qPCR analysis. Underlined genes are canonical PRC1 targets. The relative amount of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least three independent experiments. ( C ) ChIP-qPCR showing a marginal binding of canonical PRC1 (cPRC1; PCGF2) to PCGF6-bound genes with high H3K27me3 (PCGF6 +H3K27me3+/hi) and those with low H3K27me3 (PCGF6 +H3K27me3-/lo) in wild type (WT) ESCs. Eed -KO ESCs were used to confirm whether H3K27me3-dependent recruitment of cPRC1 is active at indicated gene locus. NC: negative control. ( D ) Top four de novo motif recognition hits for genes bound by PCGF6, RING1B, CBX7 (NCBI GEO accession number GSM1041373), MAX (NCBI GEO accession number GSM1171650) or MYC (NCBI GEO accession number GSM1171648) in wild type ESCs. ( E ) Expression levels of Max and Mga in untreated ESCs or those treated with control, Max siRNA or Mga siRNA revealed by RT-qPCR analysis (left). Transcription levels were normalized to a Gapdh control and are depicted as fold change relative to untreated ESCs. Error bars represent standard deviation determined from at least three independent experiments. Expression levels of FLAG-PCGF6, MAX, LAMIN B and RING1B in whole cell lysates of untreated and siRNA-treated ESCs are also shown (right). ( F ) Expression levels of the indicated genes in untreated ESCs or those treated either with control, Max siRNA or Mga siRNA. Underlined genes are canonical PRC1 targets. Expression levels were normalized to a Gapdh control and are depicted as fold change relative to mock ESCs (No treatment). Error bars represent standard deviation determined from at least three independent experiments. ( G ) Gene ontology (GO) term analysis showing that genes related to meiotic process are highly overrepresented among PCGF6+RING1B+MAX+MYC- genes. Genes were classified based on binding by PCGF6, RING1B, MAX and/or MYC and the enrichment of respective GO terms in each subset of genes was determined. The p -values for the significance of over-representation against total genes are shown along the x-axis. ( H ) Changes in local PCGF6 and MAX deposition at selected PCGF6/MAX co-bound gene that do not become de-repressed in Max -KO ESCs were determined by ChIP-qPCR using Max -KO ESCs stably expressing both an HA-tagged Pcgf6 and a Flag-tagged Max (WT or Δb) expression vectors, and are shown as described in Figure 2C . DOI: http://dx.doi.org/10.7554/eLife.21064.010

    Journal: eLife

    Article Title: PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes

    doi: 10.7554/eLife.21064

    Figure Lengend Snippet: The role of MAX/MGA in recruiting PCGF6-PRC1 to its target genes. ( A ) The expression of FLAG-tagged exogenous PCGF6 in wild type (WT) and Eed -KO ESCs. Expression levels of FLAG-tagged PCGF6 and endogenous LAMIN B protein in wild type and Eed -KO ESCs mock or FLAG-PCGF6 construct transfected were tested by immunoblotting. ( B ) Local levels of FLAG at the indicated promoter regions in wild type or Eed -KO ESCs expressing FLAG-tagged PCGF6 were determined by ChIP-qPCR analysis. Underlined genes are canonical PRC1 targets. The relative amount of ChIPed DNA is depicted as a percentage of input DNA. Error bars represent standard deviation determined from at least three independent experiments. ( C ) ChIP-qPCR showing a marginal binding of canonical PRC1 (cPRC1; PCGF2) to PCGF6-bound genes with high H3K27me3 (PCGF6 +H3K27me3+/hi) and those with low H3K27me3 (PCGF6 +H3K27me3-/lo) in wild type (WT) ESCs. Eed -KO ESCs were used to confirm whether H3K27me3-dependent recruitment of cPRC1 is active at indicated gene locus. NC: negative control. ( D ) Top four de novo motif recognition hits for genes bound by PCGF6, RING1B, CBX7 (NCBI GEO accession number GSM1041373), MAX (NCBI GEO accession number GSM1171650) or MYC (NCBI GEO accession number GSM1171648) in wild type ESCs. ( E ) Expression levels of Max and Mga in untreated ESCs or those treated with control, Max siRNA or Mga siRNA revealed by RT-qPCR analysis (left). Transcription levels were normalized to a Gapdh control and are depicted as fold change relative to untreated ESCs. Error bars represent standard deviation determined from at least three independent experiments. Expression levels of FLAG-PCGF6, MAX, LAMIN B and RING1B in whole cell lysates of untreated and siRNA-treated ESCs are also shown (right). ( F ) Expression levels of the indicated genes in untreated ESCs or those treated either with control, Max siRNA or Mga siRNA. Underlined genes are canonical PRC1 targets. Expression levels were normalized to a Gapdh control and are depicted as fold change relative to mock ESCs (No treatment). Error bars represent standard deviation determined from at least three independent experiments. ( G ) Gene ontology (GO) term analysis showing that genes related to meiotic process are highly overrepresented among PCGF6+RING1B+MAX+MYC- genes. Genes were classified based on binding by PCGF6, RING1B, MAX and/or MYC and the enrichment of respective GO terms in each subset of genes was determined. The p -values for the significance of over-representation against total genes are shown along the x-axis. ( H ) Changes in local PCGF6 and MAX deposition at selected PCGF6/MAX co-bound gene that do not become de-repressed in Max -KO ESCs were determined by ChIP-qPCR using Max -KO ESCs stably expressing both an HA-tagged Pcgf6 and a Flag-tagged Max (WT or Δb) expression vectors, and are shown as described in Figure 2C . DOI: http://dx.doi.org/10.7554/eLife.21064.010

    Article Snippet: Real-time qPCR was performed using the Brilliant III SYBR Green QPCR Master Mix (Agilent).

    Techniques: Expressing, Construct, Transfection, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Binding Assay, Negative Control, Quantitative RT-PCR, Stable Transfection

    MiR-specific qPCR on synthetic templates with DNA primers . A The effect of primer concentration on Cq value of ssc-let-7d and ssc-miR-26a miR-specific qPCR assays. Real-time PCR assays were performed in parallel at three different concentrations (125, 250 and 500 nM) of the forward and of the reverse primers. B Amplification curves of an eight log 10 dilution series of a synthetic ssc-let-7d template in the ssc-let-7d miR-specific qPCR assays. All samples contained a final concentration of 0.2 ng/μl salmon sperm DNA. C Extrapolation of Cq as function of the log 10 of the number of templates for the same experiment as in B was a straight line (R 2 = 0.9993) with slope of -3.341 (PCR efficiency = 99%) over eight log 10 dilution of the template. D Melting curve analysis of the same experiment. No template control is labeled ntc. Melting curve analysis was performed from 60°C to 99°C.

    Journal: BMC Biotechnology

    Article Title: Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers

    doi: 10.1186/1472-6750-11-70

    Figure Lengend Snippet: MiR-specific qPCR on synthetic templates with DNA primers . A The effect of primer concentration on Cq value of ssc-let-7d and ssc-miR-26a miR-specific qPCR assays. Real-time PCR assays were performed in parallel at three different concentrations (125, 250 and 500 nM) of the forward and of the reverse primers. B Amplification curves of an eight log 10 dilution series of a synthetic ssc-let-7d template in the ssc-let-7d miR-specific qPCR assays. All samples contained a final concentration of 0.2 ng/μl salmon sperm DNA. C Extrapolation of Cq as function of the log 10 of the number of templates for the same experiment as in B was a straight line (R 2 = 0.9993) with slope of -3.341 (PCR efficiency = 99%) over eight log 10 dilution of the template. D Melting curve analysis of the same experiment. No template control is labeled ntc. Melting curve analysis was performed from 60°C to 99°C.

    Article Snippet: To investigate the effect of different PCR master mixes on the performance of miR-specific qPCR with DNA primers we compared the amplification of synthetic templates with the QuantiFast SYBR Green PCR master mix (Qiagen, Germany) and the Brilliant III Ultra-Fast QPCR Master Mix (Agilent, USA).

    Techniques: Real-time Polymerase Chain Reaction, Concentration Assay, Amplification, Polymerase Chain Reaction, Labeling

    MiR-specific qPCR in different qPCR master mixes . A Comparison of amplification curves of a synthetic ssc-let-7d template in the ssc-let-7d miR-specific qPCR assay in QuantiFast and in Brilliant III qPCR Master mixes. B Melting curve analysis of the same experiment. No template control is labeled ntc. Melting curve analysis was performed from 60°C to 99°C. No change in fluorescence (dF/dT = 0) was observed above 80°C and this part of the curves was omitted from the figure. C Extrapolation of Cq as function of the log 10 of the number of templates for the same experiment as in A was a straight line (R 2 indicated on figure) and for both master mixes the PCR efficiency was 99% as calculated from the slope of the regression line.

    Journal: BMC Biotechnology

    Article Title: Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers

    doi: 10.1186/1472-6750-11-70

    Figure Lengend Snippet: MiR-specific qPCR in different qPCR master mixes . A Comparison of amplification curves of a synthetic ssc-let-7d template in the ssc-let-7d miR-specific qPCR assay in QuantiFast and in Brilliant III qPCR Master mixes. B Melting curve analysis of the same experiment. No template control is labeled ntc. Melting curve analysis was performed from 60°C to 99°C. No change in fluorescence (dF/dT = 0) was observed above 80°C and this part of the curves was omitted from the figure. C Extrapolation of Cq as function of the log 10 of the number of templates for the same experiment as in A was a straight line (R 2 indicated on figure) and for both master mixes the PCR efficiency was 99% as calculated from the slope of the regression line.

    Article Snippet: To investigate the effect of different PCR master mixes on the performance of miR-specific qPCR with DNA primers we compared the amplification of synthetic templates with the QuantiFast SYBR Green PCR master mix (Qiagen, Germany) and the Brilliant III Ultra-Fast QPCR Master Mix (Agilent, USA).

    Techniques: Real-time Polymerase Chain Reaction, Amplification, Labeling, Fluorescence, Polymerase Chain Reaction

    Discrimination between miRNAs with single nucleotide differences . A Position of the single nucleotide mismatches relative to the PCR primers for the ssc-let-7a, ssc-miR-23a, ssc-miR-125b and ssc-miR-150 qPCR assays. The ssc-miR-23b sequence used for mismatch discrimination was taken from miRBase and is different from the ssc-miR-23b sequence found in uterus and used for designing the ssc-miR-23b qPCR primers (Table 1). B Discrimination between closely related miRNA templates for miR-specific qPCR assays with DNA primers. Mismatches in the miRNA compared to the PCR primers are underlined. The data represents the results of three to four measurements. C Amplification curves of ssc-let-7a and ssc-let-7e synthetic template in the ssc-let-7a miR-specific qPCR assays. All samples including the no template control (ntc) contained a final concentration of 0.2 ng/μl salmon sperm DNA.

    Journal: BMC Biotechnology

    Article Title: Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers

    doi: 10.1186/1472-6750-11-70

    Figure Lengend Snippet: Discrimination between miRNAs with single nucleotide differences . A Position of the single nucleotide mismatches relative to the PCR primers for the ssc-let-7a, ssc-miR-23a, ssc-miR-125b and ssc-miR-150 qPCR assays. The ssc-miR-23b sequence used for mismatch discrimination was taken from miRBase and is different from the ssc-miR-23b sequence found in uterus and used for designing the ssc-miR-23b qPCR primers (Table 1). B Discrimination between closely related miRNA templates for miR-specific qPCR assays with DNA primers. Mismatches in the miRNA compared to the PCR primers are underlined. The data represents the results of three to four measurements. C Amplification curves of ssc-let-7a and ssc-let-7e synthetic template in the ssc-let-7a miR-specific qPCR assays. All samples including the no template control (ntc) contained a final concentration of 0.2 ng/μl salmon sperm DNA.

    Article Snippet: To investigate the effect of different PCR master mixes on the performance of miR-specific qPCR with DNA primers we compared the amplification of synthetic templates with the QuantiFast SYBR Green PCR master mix (Qiagen, Germany) and the Brilliant III Ultra-Fast QPCR Master Mix (Agilent, USA).

    Techniques: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Sequencing, Amplification, Concentration Assay

    Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of three independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time qPCR analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.

    Journal: Molecular and Cellular Biology

    Article Title: Evidence of a Prion-Like Transmission of p53 Amyloid in Saccharomyces cerevisiae

    doi: 10.1128/MCB.00118-17

    Figure Lengend Snippet: Loss of function of aggregated p53. (A) The level of LacZ mRNA was measured in cells with or without seeds using reverse transcription followed by real-time PCR analysis. Two independent reference genes, CDC19 and TAF10 , were used for normalization and fold change in the mRNA levels. The data represent the averages of three independent real-time PCR analyses. The error bars indicate standard deviations from the mean. (B) (Top) ChIP of p53 from cells with or without seeds. Yeast cells were analyzed by PCR and visualized by agarose gel electrophoresis. Differences in amplification were observed in input, IP, and mock IP. TAF10 was used as a nonbinding control. (Bottom) Graphical representation of chromatin immunoprecipitation of p53 displaying percent enrichment/input by real-time qPCR analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent averages of the results of three independent real-time analyses. (C) Immunofluorescence study of chromatin spread of yeast cells with or without seeds. The cells without seeds, but not those with seeds, displayed p53 in a majority of the spread as chromatin bound. Scale bar, ∼3 μm. Statistical analysis of the total percent spread was calculated as represented graphically below.

    Article Snippet: Brilliant-III UltraFast SYBR green qPCR master mix (Agilent Technologies) was used for this, according to the manufacturer's protocol.

    Techniques: Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Immunofluorescence

    Effect of P8 fibril on GFP-tagged functional p53. (A) Immunofluorescence assay to visualize p53-GFP in yeast cells with or without seeds. Aggregates of p53 are seen as green cytoplasmic focus structures specifically in the cells harboring the seeds. However, in cells without any seeds, p53-GFP was colocalized with DAPI. Scale bar, ∼5 μm. (B) Graphical representation of ChIP of p53 displaying percent enrichment/input at the p53 binding element by real-time qPCR analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent the averages of the results of three independent real-time analyses. The error bars indicate standard deviations from the mean.

    Journal: Molecular and Cellular Biology

    Article Title: Evidence of a Prion-Like Transmission of p53 Amyloid in Saccharomyces cerevisiae

    doi: 10.1128/MCB.00118-17

    Figure Lengend Snippet: Effect of P8 fibril on GFP-tagged functional p53. (A) Immunofluorescence assay to visualize p53-GFP in yeast cells with or without seeds. Aggregates of p53 are seen as green cytoplasmic focus structures specifically in the cells harboring the seeds. However, in cells without any seeds, p53-GFP was colocalized with DAPI. Scale bar, ∼5 μm. (B) Graphical representation of ChIP of p53 displaying percent enrichment/input at the p53 binding element by real-time qPCR analysis. The antibody used for ChIP was anti-p53 D0-1 (5 μg). The data represent the averages of the results of three independent real-time analyses. The error bars indicate standard deviations from the mean.

    Article Snippet: Brilliant-III UltraFast SYBR green qPCR master mix (Agilent Technologies) was used for this, according to the manufacturer's protocol.

    Techniques: Functional Assay, Immunofluorescence, Chromatin Immunoprecipitation, Binding Assay, Real-time Polymerase Chain Reaction

    Gene expression levels measured by qPCR. (A) ABA transport and biosynthesis genes expression levels. (B) Genes that respond to drought. The expression levels are relative to the normalizer gene (Pre-mRNA splicing PRP18 -interacting factor) that was identified from the in silico expression analysis. Bars represent the standard deviation of three replicates.

    Journal: Frontiers in Plant Science

    Article Title: Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns

    doi: 10.3389/fpls.2017.00216

    Figure Lengend Snippet: Gene expression levels measured by qPCR. (A) ABA transport and biosynthesis genes expression levels. (B) Genes that respond to drought. The expression levels are relative to the normalizer gene (Pre-mRNA splicing PRP18 -interacting factor) that was identified from the in silico expression analysis. Bars represent the standard deviation of three replicates.

    Article Snippet: Gene-specific primers were designed to span the selected genes using Primer3 software ( http://frodo.wi.mit.edu/primer3/ ). qPCR was carried out on 1 μL diluted cDNA by triplicate using the MaxPro3000P Stratagene Sequence Detection System, Brilliant III Ultra Fast SYBR Green QPCR master mix (Agilent) and primers at a final concentration between 250 and 450 nM.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, In Silico, Standard Deviation

    bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of three experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using RT-qPCR as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.

    Journal: The Journal of Biological Chemistry

    Article Title: Regulation of Inositol Metabolism Is Fine-tuned by Inositol Pyrophosphates in Saccharomyces cerevisiae * * ♦

    doi: 10.1074/jbc.M113.493353

    Figure Lengend Snippet: bZIP and inositol pyrophosphate kinase (DINS) domains of Kcs1 are required for INO1 transcription. A, diagram of the bZIP and the DINS functional domains of Kcs1 indicating site mutations disrupting individual domains. B, serial 10-fold dilutions of kcs1 Δ cells carrying either empty vector (pURA3), mutated bZIP domain (p kcs1 L1L2→AA ), mutated DINS domain (p kcs1 SLL→AAA ), or WT KCS1 were spotted on I− or I+ plates. Plates were incubated at 30 °C for 3 days. The figure shown is representative of three experiments. C, cells harboring the empty vector (pEV), WT KCS1, or mutated KCS1 were cultured in I+ to the mid-logarithmic phase ( A 550 of 0.5), pelleted, washed with prewarmed I+ or I−, and resuspended in fresh prewarmed I+ or I−. After the shift, cells were grown for 2 h. INO1 mRNA was quantified using RT-qPCR as described under “Experimental Procedures.” The data shown in C are the average of three experiments ± S.D.

    Article Snippet: RT-qPCRs were performed in a 20-μl volume using Brilliant III Ultra-Faster SYBR Green qPCR master mix (Agilent Technologies, Santa Clara, CA).

    Techniques: Functional Assay, Plasmid Preparation, Incubation, Cell Culture, Quantitative RT-PCR

    mCMV-infected Siglec-H KO mice exhibit a strong up-regulation of type-I IFN response genes 26 wk after infection. (A) RNA from splenic cells of mCMV-infected WT (wt) or Siglec-H KO (ko) mice and noninfected controls were isolated, and mRNA expression of different type I IFN–inducible genes was measured by qRT-PCR relative to mCMV-infected WT mice, whose expression levels were set to 1. Actin served as a housekeeping gene. Relative mRNA levels of IRF7 and CXCL10 10 wk after mCMV infection and 26 wk after mCMV infection are shown. Data are representative of two independent experiments ( n = 6 for each experiment). **, P

    Journal: The Journal of Experimental Medicine

    Article Title: Siglec-H protects from virus-triggered severe systemic autoimmunity

    doi: 10.1084/jem.20160189

    Figure Lengend Snippet: mCMV-infected Siglec-H KO mice exhibit a strong up-regulation of type-I IFN response genes 26 wk after infection. (A) RNA from splenic cells of mCMV-infected WT (wt) or Siglec-H KO (ko) mice and noninfected controls were isolated, and mRNA expression of different type I IFN–inducible genes was measured by qRT-PCR relative to mCMV-infected WT mice, whose expression levels were set to 1. Actin served as a housekeeping gene. Relative mRNA levels of IRF7 and CXCL10 10 wk after mCMV infection and 26 wk after mCMV infection are shown. Data are representative of two independent experiments ( n = 6 for each experiment). **, P

    Article Snippet: Gene expression by quantitative RT-PCR (qRT-PCR) For qRT-PCR, RNA from 107 splenic cells was isolated by using QIAshredder and RNeasy kits (QIAGEN) according to the manufacturer’s instructions. cDNA was synthesized using RNase H-Reverse transcription (Superscript III; Invitrogen), and qRT-PCR was performed on a quantitative PCR system (Stratagene Mx3000P) with green quantitative PCR Master Mix (Brilliant III Ultra-Fast SYBR; Agilent Technologies). mRNA expression of different type I IFN–inducible genes was measured by qRT-PCR relative to mCMV-infected WT mice, whose expression levels were set to 1.

    Techniques: Infection, Mouse Assay, Isolation, Expressing, Quantitative RT-PCR

    Genes involved in sulfur metabolism are repressed by Pos19 upon 1 O 2 stress. (A) Plasmid-borne over-expression of Pos19. The pos19 gene together with its native RpoE-dependent promoter was cloned into middle-copy plasmid pBBR1 and expressed in R . sphaeroides wild-type 2.4.1 cells (pPos19). Additionally, Pos19 was over-expressed with mutations in codon 16 and start codon 1 ( Fig 2A ). Wild-type cells carrying empty vector pBBR1 served as a control (pBBR1). Strains were subjected to 1 O 2 stress experiments and samples (collected at 0 and 7 min) used for Northern blot analysis. The 5S rRNA was probed as a loading control. (B) Microarray results for genes involved in sulfur metabolism and the most down-regulated mRNA RSP_0557. Samples from the Pos19 over-expression strain (pPos19) were collected after 7 min of 1 O 2 stress and compared to an empty vector control (pBBR1) by microarray analysis (blue bars). In a second microarray analysis, samples from stressed R . sphaeroides wild-type 2.4.1 cells (7 min 1 O 2 ) were compared to unstressed cells (grey bars) [ 28 ]. Effects on mRNA levels were calculated as log 2 ratios. Values represent the mean from two individual microarray analyses, each containing pooled biological triplicates per strain. (C) Induction of selected genes by qRT-PCR. Empty vector control (pBBR1) and over-expression strains (pPos19 and pThr1) were subjected to 1 O 2 stress experiments with samples collected at time points 0 and 7 min of stress. Selected mRNA levels in stress samples (7 min) were calculated relative to unstressed samples (0 min) as log 2 ratios, using rpoZ as a control gene. Results were obtained from three independent biological experiments. Error bars represent the standard error of mean.

    Journal: PLoS ONE

    Article Title: Characteristics of Pos19 – A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides

    doi: 10.1371/journal.pone.0163425

    Figure Lengend Snippet: Genes involved in sulfur metabolism are repressed by Pos19 upon 1 O 2 stress. (A) Plasmid-borne over-expression of Pos19. The pos19 gene together with its native RpoE-dependent promoter was cloned into middle-copy plasmid pBBR1 and expressed in R . sphaeroides wild-type 2.4.1 cells (pPos19). Additionally, Pos19 was over-expressed with mutations in codon 16 and start codon 1 ( Fig 2A ). Wild-type cells carrying empty vector pBBR1 served as a control (pBBR1). Strains were subjected to 1 O 2 stress experiments and samples (collected at 0 and 7 min) used for Northern blot analysis. The 5S rRNA was probed as a loading control. (B) Microarray results for genes involved in sulfur metabolism and the most down-regulated mRNA RSP_0557. Samples from the Pos19 over-expression strain (pPos19) were collected after 7 min of 1 O 2 stress and compared to an empty vector control (pBBR1) by microarray analysis (blue bars). In a second microarray analysis, samples from stressed R . sphaeroides wild-type 2.4.1 cells (7 min 1 O 2 ) were compared to unstressed cells (grey bars) [ 28 ]. Effects on mRNA levels were calculated as log 2 ratios. Values represent the mean from two individual microarray analyses, each containing pooled biological triplicates per strain. (C) Induction of selected genes by qRT-PCR. Empty vector control (pBBR1) and over-expression strains (pPos19 and pThr1) were subjected to 1 O 2 stress experiments with samples collected at time points 0 and 7 min of stress. Selected mRNA levels in stress samples (7 min) were calculated relative to unstressed samples (0 min) as log 2 ratios, using rpoZ as a control gene. Results were obtained from three independent biological experiments. Error bars represent the standard error of mean.

    Article Snippet: Real-time RT-PCR reactions were prepared using the Brilliant III Ultra-Fast SYBR Green QRT-PCR Master Mix (Agilent) with total RNA in a final concentration of 4 ng μl−1 .

    Techniques: Plasmid Preparation, Over Expression, Clone Assay, Northern Blot, Microarray, Quantitative RT-PCR