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  • 94
    Millipore expand long template pcr system
    Expand Long Template Pcr System, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche expand long template polymerase chain reaction pcr system
    Analysis of the PA2231-2245 gene cluster by <t>RT-PCR</t> of intergenic regions. Lane 1, size markers; lane 2, PCR amplification product of PA2230-2231 cluster with genomic <t>DNA</t> as the template (this serves as a control for RT-PCR of this region); lane 3, RT-PCR of PA2230 and -2231 (the lack of product indicates that PA2230 and -2231 are not cotranscribed); lane 4, size marker; lane 5, RT-PCR of PA2231 and -2232; lane 6, PA2232 and -2233; lane 7, PA2233 and -2234; lane 8, PA2234 and -2235; lane 9, PA2235 and -2236; lane 10, PA2236 and -2237; lane 11, PA2237 and -2238; lane 12, PA2238 and -2239; lane 13, PA2239 and -2240; lane 14, PA2240 and -2241; lane 15, PA2241 and -2242; lane 16, PA2242 and -2243; lane 17, PA2243 and -2244; lane 18, PA2244 and -2245. Control experiments without reverse transcriptase reactions prior to PCR were negative.
    Expand Long Template Polymerase Chain Reaction Pcr System, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 58 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche template polymerase chain reaction pcr system
    Analysis of the PA2231-2245 gene cluster by <t>RT-PCR</t> of intergenic regions. Lane 1, size markers; lane 2, PCR amplification product of PA2230-2231 cluster with genomic <t>DNA</t> as the template (this serves as a control for RT-PCR of this region); lane 3, RT-PCR of PA2230 and -2231 (the lack of product indicates that PA2230 and -2231 are not cotranscribed); lane 4, size marker; lane 5, RT-PCR of PA2231 and -2232; lane 6, PA2232 and -2233; lane 7, PA2233 and -2234; lane 8, PA2234 and -2235; lane 9, PA2235 and -2236; lane 10, PA2236 and -2237; lane 11, PA2237 and -2238; lane 12, PA2238 and -2239; lane 13, PA2239 and -2240; lane 14, PA2240 and -2241; lane 15, PA2241 and -2242; lane 16, PA2242 and -2243; lane 17, PA2243 and -2244; lane 18, PA2244 and -2245. Control experiments without reverse transcriptase reactions prior to PCR were negative.
    Template Polymerase Chain Reaction Pcr System, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim expand long template pcr
    Amplification of the TRS-1 subrepeat element produced 21 <t>PCR</t> types from 101 clinical isolates of T. rubrum . (PCR type 1+ from strain CBS 303.38 is not shown). PCR types 1 through 6 represent strains with 1 to 6 copies of TRS-1 in the <t>NTS.</t> The copy number and chromosomal distribution of TRS-1 in strains with complex pattern types 7 through 20 are undetermined. M, molecular weight marker.
    Expand Long Template Pcr, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 88/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim expand long template pcr kit
    Infection with CNS-derived HIV and FIV strains increases MMP expression in primary macrophages. MMP-2 and -9 protein (A, C) and RNA (B, D) levels were assessed by gelatin zymography and semiquantitative <t>RT-PCR</t> at days 0, 1, 3, 5, and 7 postinfection using conditioned media from uninfected and JRCSF-infected human macrophages (A, B) and uninfected and V 1 CSF-infected feline macrophages (C, D). Infection with either virus induced concurrent increases in MMP-2 and -9 protein and mRNA expression that increased with viral replication. Viral replication was measured by RT-PCR amplification of the HIV-1 gag gene or the FIV pol gene using RNA from human and feline <t>PBMC</t> infected with HIV or FIV as positive controls (+). Conditioned medium and RNA from stimulated human macrophages served as controls for detection of MMP expression (+). Amplification of GAPDH was used to ensure equal template loading.
    Expand Long Template Pcr Kit, supplied by Boehringer Mannheim, 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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    91
    Roche expand long template pcr kit
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Kit, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 480 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche expand long template pcr systemkit
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Systemkit, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche expand long template pcr polymerase
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Polymerase, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad expand long template pcr system
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr System, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche expand long template pcr reagent
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Reagent, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche expand long template pcr buffer 3
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Buffer 3, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim expand long template pcr polymerase
    Characterization and suitability of the <t>HEMn</t> cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of <t>PCR</t> fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p
    Expand Long Template Pcr Polymerase, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Analysis of the PA2231-2245 gene cluster by RT-PCR of intergenic regions. Lane 1, size markers; lane 2, PCR amplification product of PA2230-2231 cluster with genomic DNA as the template (this serves as a control for RT-PCR of this region); lane 3, RT-PCR of PA2230 and -2231 (the lack of product indicates that PA2230 and -2231 are not cotranscribed); lane 4, size marker; lane 5, RT-PCR of PA2231 and -2232; lane 6, PA2232 and -2233; lane 7, PA2233 and -2234; lane 8, PA2234 and -2235; lane 9, PA2235 and -2236; lane 10, PA2236 and -2237; lane 11, PA2237 and -2238; lane 12, PA2238 and -2239; lane 13, PA2239 and -2240; lane 14, PA2240 and -2241; lane 15, PA2241 and -2242; lane 16, PA2242 and -2243; lane 17, PA2243 and -2244; lane 18, PA2244 and -2245. Control experiments without reverse transcriptase reactions prior to PCR were negative.

    Journal: Journal of Bacteriology

    Article Title: Putative Exopolysaccharide Synthesis Genes Influence Pseudomonas aeruginosa Biofilm Development

    doi: 10.1128/JB.186.14.4449-4456.2004

    Figure Lengend Snippet: Analysis of the PA2231-2245 gene cluster by RT-PCR of intergenic regions. Lane 1, size markers; lane 2, PCR amplification product of PA2230-2231 cluster with genomic DNA as the template (this serves as a control for RT-PCR of this region); lane 3, RT-PCR of PA2230 and -2231 (the lack of product indicates that PA2230 and -2231 are not cotranscribed); lane 4, size marker; lane 5, RT-PCR of PA2231 and -2232; lane 6, PA2232 and -2233; lane 7, PA2233 and -2234; lane 8, PA2234 and -2235; lane 9, PA2235 and -2236; lane 10, PA2236 and -2237; lane 11, PA2237 and -2238; lane 12, PA2238 and -2239; lane 13, PA2239 and -2240; lane 14, PA2240 and -2241; lane 15, PA2241 and -2242; lane 16, PA2242 and -2243; lane 17, PA2243 and -2244; lane 18, PA2244 and -2245. Control experiments without reverse transcriptase reactions prior to PCR were negative.

    Article Snippet: DNA contamination of the purified RNA was assessed by Expand long-template PCR using rplU primers.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Marker

    Deletion of SAMHD1 does not affect mtDNA stability. a) MtDNA copy number in the TA muscle of 5 or 6 wt (filled dots) and SAMHD1 −/− (open dots) 13-week-old (adult), 1-year-old (old adult), and 2-year-old (aged) animals was determined by qPCR and normalized to the value for adult wt mice. The mean for each group is indicated by a horizontal line. The p-values were calculated using Welch’s t-test; ns, non-significant. b) DNA isolated from embryos and from the TA muscle of pups, adults, 1-year-old (old) adults, or aged animals was linearized with SacI endonuclease and separated on a neutral gel. MtDNA was visualized as above. Full-length mtDNA is indicated (FL); the asterisk denotes a higher-migrating species resistant to cleavage. c) Long-range PCR to detect deletions in mtDNA from the TA muscle of wt mice of various ages. Full-length product is indicated (FL). Only minor species containing deletions are observed in the mtDNA from old adults and aged animals, as indicated by the vertical line on the right-hand side of the gel. d) Untreated or alkali-treated DNA from skeletal muscle of aged wt and SAMHD1 −/− (ko) mice was analyzed on a denaturing gel, and mtDNA was visualized using a COX1 probe. Each sample lane corresponds to an individual mouse, and dotted lines represent the median. e) The median length of the untreated mtDNA in samples from Fig. 5d is indicated by a horizontal line. The two groups were compared using Welch’s t-test (ns, non-significant; n = 4). f) The length difference between untreated and alkali-treated mtDNAs shown in Fig. 5d was used to compute the number of rNMPs per single strand of mtDNA. The horizontal lines indicate the median. The p-value of the statistically significant difference between the two groups was calculated by Welch’s t-test; n = 4. g) Long-range PCR was performed on mtDNA isolated from the TA muscle of adult and aged wt or SAMHD1 −/− (ko) mice. FL, full-length product; the vertical line indicates the size range of mtDNA molecules with deletions. h) Kaplan–Meier survival curve for wt and SAMHD1 −/− (ko) mice. Comparison of the curves by the log-rank (Mantel–Cox) test confirmed no statistically significant difference between the genotypes. The sizes of the bands in the DNA ladder are indicated in kb. See also Fig. S5.

    Journal: bioRxiv

    Article Title: The physiological level of rNMPs present in mtDNA does not compromise its stability

    doi: 10.1101/746719

    Figure Lengend Snippet: Deletion of SAMHD1 does not affect mtDNA stability. a) MtDNA copy number in the TA muscle of 5 or 6 wt (filled dots) and SAMHD1 −/− (open dots) 13-week-old (adult), 1-year-old (old adult), and 2-year-old (aged) animals was determined by qPCR and normalized to the value for adult wt mice. The mean for each group is indicated by a horizontal line. The p-values were calculated using Welch’s t-test; ns, non-significant. b) DNA isolated from embryos and from the TA muscle of pups, adults, 1-year-old (old) adults, or aged animals was linearized with SacI endonuclease and separated on a neutral gel. MtDNA was visualized as above. Full-length mtDNA is indicated (FL); the asterisk denotes a higher-migrating species resistant to cleavage. c) Long-range PCR to detect deletions in mtDNA from the TA muscle of wt mice of various ages. Full-length product is indicated (FL). Only minor species containing deletions are observed in the mtDNA from old adults and aged animals, as indicated by the vertical line on the right-hand side of the gel. d) Untreated or alkali-treated DNA from skeletal muscle of aged wt and SAMHD1 −/− (ko) mice was analyzed on a denaturing gel, and mtDNA was visualized using a COX1 probe. Each sample lane corresponds to an individual mouse, and dotted lines represent the median. e) The median length of the untreated mtDNA in samples from Fig. 5d is indicated by a horizontal line. The two groups were compared using Welch’s t-test (ns, non-significant; n = 4). f) The length difference between untreated and alkali-treated mtDNAs shown in Fig. 5d was used to compute the number of rNMPs per single strand of mtDNA. The horizontal lines indicate the median. The p-value of the statistically significant difference between the two groups was calculated by Welch’s t-test; n = 4. g) Long-range PCR was performed on mtDNA isolated from the TA muscle of adult and aged wt or SAMHD1 −/− (ko) mice. FL, full-length product; the vertical line indicates the size range of mtDNA molecules with deletions. h) Kaplan–Meier survival curve for wt and SAMHD1 −/− (ko) mice. Comparison of the curves by the log-rank (Mantel–Cox) test confirmed no statistically significant difference between the genotypes. The sizes of the bands in the DNA ladder are indicated in kb. See also Fig. S5.

    Article Snippet: MtDNA deletion analysis by long-range PCR The Expand Long Template PCR system (Roche) with forward and reverse primers at nt 2,478–2,512 and nt 1,933–1,906, respectively, was used to amplify a ~15,800 bp fragment of mouse mtDNA from 25 ng of total DNA.

    Techniques: Real-time Polymerase Chain Reaction, Mouse Assay, Isolation, Polymerase Chain Reaction

    Generation and analysis of Δ tku70 Δ lcc1 knockout strains. a Schematic presentation of the Δ tku70 Δ lcc1 and lcc1 -WT loci, indicating the location of the primers and restriction sites used for analysis of the transformants. b PCR analysis results of seven Δ tku70 Δ lcc1 strains and the WT with primers G/J (Table 1 ), showing a 5.0 kb band for the WT and a 5.3 kb band for the knockout strains (only 7 out of the 32 Δ tku70 Δ lcc1 strains are shown here). M molecular weight marker (1 kb ladder, Fermentas). c Southern analysis of seven Δ tku70 Δ lcc1 strains. Genomic DNA was digested with Xba I and hybridization with the probe (amplified with primers G/L) showed a 1.4 kb band for the WT strain and a 3.1 kb band for the knockout strains

    Journal: Current Genetics

    Article Title: Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation

    doi: 10.1007/s00294-010-0322-2

    Figure Lengend Snippet: Generation and analysis of Δ tku70 Δ lcc1 knockout strains. a Schematic presentation of the Δ tku70 Δ lcc1 and lcc1 -WT loci, indicating the location of the primers and restriction sites used for analysis of the transformants. b PCR analysis results of seven Δ tku70 Δ lcc1 strains and the WT with primers G/J (Table 1 ), showing a 5.0 kb band for the WT and a 5.3 kb band for the knockout strains (only 7 out of the 32 Δ tku70 Δ lcc1 strains are shown here). M molecular weight marker (1 kb ladder, Fermentas). c Southern analysis of seven Δ tku70 Δ lcc1 strains. Genomic DNA was digested with Xba I and hybridization with the probe (amplified with primers G/L) showed a 1.4 kb band for the WT strain and a 3.1 kb band for the knockout strains

    Article Snippet: From the resulting plasmid pVCKU70, the 6.1 kb linear tku70 deletion cassette was amplified with primers E/F (Table ) using the Long Template Expand PCR System (Roche, Indianapolis, IN, USA) and PCR conditions according to the manufacturer’s instructions.

    Techniques: Knock-Out, Polymerase Chain Reaction, Molecular Weight, Marker, Hybridization, Amplification

    Generation and analysis of Δ tku70 knockout strains. a Schematic presentation of the Δ tku70 and tku70 -WT loci, indicating the location of the primers and restriction sites used for analysis of the transformants. b PCR analysis of the Δ tku70 strains and the WT with primers E/F (Table 1 ), showing a 5.1 kb band for the WT and a 6.1 kb band for the knockout strains B14 and C146. M molecular weight marker (1 kb ladder, Fermentas, St. Leon-Rot, Germany). c Southern analysis of the Δ tku70 strains. Genomic DNA was digested with Eco RI and hybridization with the probe (amplified with primers E/K) showed a > 10 kb band for the WT strain and a 3.0/3.2 kb double band for the knockout strains

    Journal: Current Genetics

    Article Title: Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation

    doi: 10.1007/s00294-010-0322-2

    Figure Lengend Snippet: Generation and analysis of Δ tku70 knockout strains. a Schematic presentation of the Δ tku70 and tku70 -WT loci, indicating the location of the primers and restriction sites used for analysis of the transformants. b PCR analysis of the Δ tku70 strains and the WT with primers E/F (Table 1 ), showing a 5.1 kb band for the WT and a 6.1 kb band for the knockout strains B14 and C146. M molecular weight marker (1 kb ladder, Fermentas, St. Leon-Rot, Germany). c Southern analysis of the Δ tku70 strains. Genomic DNA was digested with Eco RI and hybridization with the probe (amplified with primers E/K) showed a > 10 kb band for the WT strain and a 3.0/3.2 kb double band for the knockout strains

    Article Snippet: From the resulting plasmid pVCKU70, the 6.1 kb linear tku70 deletion cassette was amplified with primers E/F (Table ) using the Long Template Expand PCR System (Roche, Indianapolis, IN, USA) and PCR conditions according to the manufacturer’s instructions.

    Techniques: Knock-Out, Polymerase Chain Reaction, Molecular Weight, Marker, Hybridization, Amplification

    Isolation of cDNA corresponding to 5′ end of 4.6-kb Sbe1c transcript. A, Schematic illustration of the 4.6-kb Sbe1c transcript and product obtained from 5′-RACE analysis. Start of pRN60 sequence and location of PCR primers used in the 5′-RACE and RT-PCR reactions are indicated. B, Gel analysis of 5′-RACE products obtained in reactions with primers indicated and poly(A + ) RNA prepared from 12-d-old wheat kernels. Arrow indicates migration of product carrying the 5′ end of the 4.6-kb Sbe1c cDNA. Migration of standard DNA fragments are indicated to the right. C, Gel analysis of RT-PCR products obtained from reactions with PCR primers BE65 and BE38.

    Journal: Plant Physiology

    Article Title: Isolation of a cDNA Encoding a Granule-Bound 152-Kilodalton Starch-Branching Enzyme in Wheat 1

    doi:

    Figure Lengend Snippet: Isolation of cDNA corresponding to 5′ end of 4.6-kb Sbe1c transcript. A, Schematic illustration of the 4.6-kb Sbe1c transcript and product obtained from 5′-RACE analysis. Start of pRN60 sequence and location of PCR primers used in the 5′-RACE and RT-PCR reactions are indicated. B, Gel analysis of 5′-RACE products obtained in reactions with primers indicated and poly(A + ) RNA prepared from 12-d-old wheat kernels. Arrow indicates migration of product carrying the 5′ end of the 4.6-kb Sbe1c cDNA. Migration of standard DNA fragments are indicated to the right. C, Gel analysis of RT-PCR products obtained from reactions with PCR primers BE65 and BE38.

    Article Snippet: PCR reactions (25 μL) were performed with a 0.5-μL aliquot of the first-strand cDNA using the Long Expand Template PCR System (Roche Diagnostics Gmbh, Mannheim, Germany) and the primer pair BE65/BE38 (Figs. and ).

    Techniques: Isolation, Sequencing, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Migration

    Amplification of the TRS-1 subrepeat element produced 21 PCR types from 101 clinical isolates of T. rubrum . (PCR type 1+ from strain CBS 303.38 is not shown). PCR types 1 through 6 represent strains with 1 to 6 copies of TRS-1 in the NTS. The copy number and chromosomal distribution of TRS-1 in strains with complex pattern types 7 through 20 are undetermined. M, molecular weight marker.

    Journal: Journal of Clinical Microbiology

    Article Title: Strain Identification of Trichophyton rubrum by Specific Amplification of Subrepeat Elements in the Ribosomal DNA Nontranscribed Spacer

    doi:

    Figure Lengend Snippet: Amplification of the TRS-1 subrepeat element produced 21 PCR types from 101 clinical isolates of T. rubrum . (PCR type 1+ from strain CBS 303.38 is not shown). PCR types 1 through 6 represent strains with 1 to 6 copies of TRS-1 in the NTS. The copy number and chromosomal distribution of TRS-1 in strains with complex pattern types 7 through 20 are undetermined. M, molecular weight marker.

    Article Snippet: The NTS region of T. rubrum NCPF 295 was amplified using the Expand Long Template PCR system (Boehringer Mannheim UK Ltd., Lewes, East Sussex, United Kingdom).

    Techniques: Amplification, Produced, Polymerase Chain Reaction, Molecular Weight, Marker

    Amplification of the TRS-2 subrepeat element, using primers TrNTSR-1 and TrNTSC-1. A 502-bp product (lane 1) representing two complete copies of TRS-2 was amplified from 86% of all isolates. Variation in the TRS-2 fragment occurred mainly in strains with a single copy of TRS-1 (PCR type 1). Lanes: 1, NCPF 295; 2, 97-12329; 3, 97-12444; 4, 97-12912; 5, 97-13550; 6, 97-14358; 7, 98-8070; 8, CBS 303.38; 9, FMG 1063; 10, 97-N393; 11, 97-14166; 12, 98-5693. M, molecular weight marker.

    Journal: Journal of Clinical Microbiology

    Article Title: Strain Identification of Trichophyton rubrum by Specific Amplification of Subrepeat Elements in the Ribosomal DNA Nontranscribed Spacer

    doi:

    Figure Lengend Snippet: Amplification of the TRS-2 subrepeat element, using primers TrNTSR-1 and TrNTSC-1. A 502-bp product (lane 1) representing two complete copies of TRS-2 was amplified from 86% of all isolates. Variation in the TRS-2 fragment occurred mainly in strains with a single copy of TRS-1 (PCR type 1). Lanes: 1, NCPF 295; 2, 97-12329; 3, 97-12444; 4, 97-12912; 5, 97-13550; 6, 97-14358; 7, 98-8070; 8, CBS 303.38; 9, FMG 1063; 10, 97-N393; 11, 97-14166; 12, 98-5693. M, molecular weight marker.

    Article Snippet: The NTS region of T. rubrum NCPF 295 was amplified using the Expand Long Template PCR system (Boehringer Mannheim UK Ltd., Lewes, East Sussex, United Kingdom).

    Techniques: Amplification, Polymerase Chain Reaction, Molecular Weight, Marker

    RT-PCR analysis of ShPMCA expression during the E-E cycle. (A) RT-PCR amplification products from total RNA isolated from vegetative cells (a), starved cells (b), precystic cells (c), 3-day-old cysts (d), 3-week-old cysts (e*), and excysting cells

    Journal:

    Article Title: Proposed Function of the Accumulation of Plasma Membrane-Type Ca2+-ATPase mRNA in Resting Cysts of the Ciliate Sterkiella histriomuscorum

    doi: 10.1128/EC.4.1.103-110.2005

    Figure Lengend Snippet: RT-PCR analysis of ShPMCA expression during the E-E cycle. (A) RT-PCR amplification products from total RNA isolated from vegetative cells (a), starved cells (b), precystic cells (c), 3-day-old cysts (d), 3-week-old cysts (e*), and excysting cells

    Article Snippet: To amplify the 3.9-kb ShPMCA gene, two rounds of PCR using the Long Expand Template PCR system (Boehringer Mannheim, Mannheim, Germany) were performed according to the manufacturer's instructions with 100 ng of genomic DNA circularized as described previously ( ).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Amplification, Isolation

    Infection with CNS-derived HIV and FIV strains increases MMP expression in primary macrophages. MMP-2 and -9 protein (A, C) and RNA (B, D) levels were assessed by gelatin zymography and semiquantitative RT-PCR at days 0, 1, 3, 5, and 7 postinfection using conditioned media from uninfected and JRCSF-infected human macrophages (A, B) and uninfected and V 1 CSF-infected feline macrophages (C, D). Infection with either virus induced concurrent increases in MMP-2 and -9 protein and mRNA expression that increased with viral replication. Viral replication was measured by RT-PCR amplification of the HIV-1 gag gene or the FIV pol gene using RNA from human and feline PBMC infected with HIV or FIV as positive controls (+). Conditioned medium and RNA from stimulated human macrophages served as controls for detection of MMP expression (+). Amplification of GAPDH was used to ensure equal template loading.

    Journal: Journal of Virology

    Article Title: Lentivirus Infection in the Brain Induces Matrix Metalloproteinase Expression: Role of Envelope Diversity

    doi:

    Figure Lengend Snippet: Infection with CNS-derived HIV and FIV strains increases MMP expression in primary macrophages. MMP-2 and -9 protein (A, C) and RNA (B, D) levels were assessed by gelatin zymography and semiquantitative RT-PCR at days 0, 1, 3, 5, and 7 postinfection using conditioned media from uninfected and JRCSF-infected human macrophages (A, B) and uninfected and V 1 CSF-infected feline macrophages (C, D). Infection with either virus induced concurrent increases in MMP-2 and -9 protein and mRNA expression that increased with viral replication. Viral replication was measured by RT-PCR amplification of the HIV-1 gag gene or the FIV pol gene using RNA from human and feline PBMC infected with HIV or FIV as positive controls (+). Conditioned medium and RNA from stimulated human macrophages served as controls for detection of MMP expression (+). Amplification of GAPDH was used to ensure equal template loading.

    Article Snippet: Genomic DNA from feline PBMC persistently infected with V1 CSF was amplified using an Expand Long Template PCR kit (Boehringer Mannheim) for 1 cycle (94°C for 1 min), 30 cycles (94°C for 1 min, 50°C for 1 min, and 68°C for 5 min), and 1 cycle (68°C for 10 min) with primers 5′-TTA G GG TAC CTG GAA TAA CAG-3′ and 5′-TCG TAA ACA GTC CCT AGT CCA TAA-3′.

    Techniques: Infection, Derivative Assay, Expressing, Zymography, Reverse Transcription Polymerase Chain Reaction, Amplification

    Characterization and suitability of the HEMn cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of PCR fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p

    Journal: Genome Research

    Article Title: HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

    doi: 10.1101/gr.128652.111

    Figure Lengend Snippet: Characterization and suitability of the HEMn cell system: The OCA2 gene is differentially expressed in HEMn-LP and HEMn-DP cells. ( A ) overview of the OCA2 - HERC2 locus ( top panel). ( Middle panel) The region covered on BAC RP11-1365A12. Vertebrate conservation (green); the position of rs12913832 (red). ( Lower panel) A schematic overview of the region investigated in this study. Restriction enzyme digestion sites are indicated. ( B ) Sequence analysis of the region around HERC2 rs12913832 in HEMn-LP ( left ) and HEMn-DP ( right ). The genotypes of rs12913832 were determined by direct sequencing of PCR fragments containing rs12913832. ( C ) RT-qPCR analysis of OCA2 primary transcripts in MCF7 and HEMn cells demonstrates differential OCA2 expression between HEMn-LP and HEMn-DP cells. Each gene expression analysis is carried out in triplicate and normalized to an endogenous reference gene ( ACTB ). ( D ) ChIP-qPCR of RNA Pol II binding at the OCA2 promoter in MCF7, HEMn-LP, and HEMn-DP cells. Enrichment is calculated relative to necdin ( NDN ), and values are normalized to input measurements. All ChIP analyses are performed in triplicate. Data are represented as mean ± SEM; (*) p

    Article Snippet: A 1450-bp fragment surrounding rs12913832 was PCR-amplified from genomic DNA obtained from HEMn-LP (C-allele) or HEMn-DP (T-allele) using the Expand Long Template PCR Kit (Roche).

    Techniques: BAC Assay, Sequencing, Polymerase Chain Reaction, Quantitative RT-PCR, Expressing, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Binding Assay

    FAIRE analysis of pigmentation-associated SNPs other than HERC2 rs12913832 present within the 3′ HERC2 /5′ OCA2 region does not reveal additional regulatory elements. ( Left ) of the investigated 3′ HERC2/ 5′ OCA2 region. Pigmentation-associated SNPs (red); linked SNPs ( r 2 > 0.8) (black). The approximate location of the analyzed PCR amplicons is indicated. ( Right side) The genotype of each SNP for HEMn-LP and HEMn-DP. The enrichments displayed are relative to NDN . Data are represented as mean ± SEM.

    Journal: Genome Research

    Article Title: HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

    doi: 10.1101/gr.128652.111

    Figure Lengend Snippet: FAIRE analysis of pigmentation-associated SNPs other than HERC2 rs12913832 present within the 3′ HERC2 /5′ OCA2 region does not reveal additional regulatory elements. ( Left ) of the investigated 3′ HERC2/ 5′ OCA2 region. Pigmentation-associated SNPs (red); linked SNPs ( r 2 > 0.8) (black). The approximate location of the analyzed PCR amplicons is indicated. ( Right side) The genotype of each SNP for HEMn-LP and HEMn-DP. The enrichments displayed are relative to NDN . Data are represented as mean ± SEM.

    Article Snippet: A 1450-bp fragment surrounding rs12913832 was PCR-amplified from genomic DNA obtained from HEMn-LP (C-allele) or HEMn-DP (T-allele) using the Expand Long Template PCR Kit (Roche).

    Techniques: Polymerase Chain Reaction