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Illumina Inc hiv 2 primer
HIV-1 demonstrates higher G-to-A hypermutant frequencies than <t>HIV-2.</t> a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p
Hiv 2 Primer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

Journal: Retrovirology

doi: 10.1186/s12977-015-0180-6

HIV-1 demonstrates higher G-to-A hypermutant frequencies than HIV-2. a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p
Figure Legend Snippet: HIV-1 demonstrates higher G-to-A hypermutant frequencies than HIV-2. a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

Techniques Used: Plasmid Preparation, DNA Sequencing, Standard Deviation

HIV-1 and HIV-2 mutation frequencies and spectra are similar in the absence of G-to-A hypermutation. a Analysis of mutation frequency in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation frequencies were determined either including or excluding G-to-A hypermutants, with the results superimposed. The relative percentage of the total data that can be attributed (or not attributed) to G-to-A hypermutation is indicated within the bars . b Analysis of HIV-1 and HIV-2 mutation spectra in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation spectra were examined after excluding all G-to-A hypermutants. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage. Data in both panels represent the mean of three experimental replicates.
Figure Legend Snippet: HIV-1 and HIV-2 mutation frequencies and spectra are similar in the absence of G-to-A hypermutation. a Analysis of mutation frequency in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation frequencies were determined either including or excluding G-to-A hypermutants, with the results superimposed. The relative percentage of the total data that can be attributed (or not attributed) to G-to-A hypermutation is indicated within the bars . b Analysis of HIV-1 and HIV-2 mutation spectra in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation spectra were examined after excluding all G-to-A hypermutants. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage. Data in both panels represent the mean of three experimental replicates.

Techniques Used: Mutagenesis

Experimental strategy for investigating HIV-1 and HIV-2 mutagenesis by Illumina DNA sequencing. Vector virus stocks were produced by co-transfecting 293T cells with HIV-1 or HIV-2 Env-deficient vectors and HIV-1 or HIV-2 CXCR4-tropic Env expression constructs. Virus stocks were concentrated, DNase I-treated to reduce plasmid carryover, and titered in U373-MAGI cells. To prepare samples for Illumina sequencing, 1 × 10 6 U373-MAGI cells were infected at an MOI of 1.0, generating approximately 1 × 10 6 proviruses per experimental replicate. This assay represents a single round of viral replication, as producer cells and target cells cannot be re-infected, due to a lack of receptor or Env expression, respectively. Polymerase chain reaction (PCR) of five amplicons (Gag, Vif, HSA, EGFP-1, and EGFP-2) was performed from the proviral DNA. Amplicons from the HIV-1 and HIV-2 proviral DNAs were either identical (HSA, EGFP-1 and 2) or homologous (Gag and Vif) in sequence. The EGFP-1 and EGFP-2 amplicons represent non-overlapping segments of the egfp gene. Sequencing libraries were prepared from the amplicons, pooled in an equimolar fashion to normalize coverage, and subjected to 2 ×150 bp sequencing on the Illumina MiSeq, generating approximately 4.7 million read pairs after data processing.
Figure Legend Snippet: Experimental strategy for investigating HIV-1 and HIV-2 mutagenesis by Illumina DNA sequencing. Vector virus stocks were produced by co-transfecting 293T cells with HIV-1 or HIV-2 Env-deficient vectors and HIV-1 or HIV-2 CXCR4-tropic Env expression constructs. Virus stocks were concentrated, DNase I-treated to reduce plasmid carryover, and titered in U373-MAGI cells. To prepare samples for Illumina sequencing, 1 × 10 6 U373-MAGI cells were infected at an MOI of 1.0, generating approximately 1 × 10 6 proviruses per experimental replicate. This assay represents a single round of viral replication, as producer cells and target cells cannot be re-infected, due to a lack of receptor or Env expression, respectively. Polymerase chain reaction (PCR) of five amplicons (Gag, Vif, HSA, EGFP-1, and EGFP-2) was performed from the proviral DNA. Amplicons from the HIV-1 and HIV-2 proviral DNAs were either identical (HSA, EGFP-1 and 2) or homologous (Gag and Vif) in sequence. The EGFP-1 and EGFP-2 amplicons represent non-overlapping segments of the egfp gene. Sequencing libraries were prepared from the amplicons, pooled in an equimolar fashion to normalize coverage, and subjected to 2 ×150 bp sequencing on the Illumina MiSeq, generating approximately 4.7 million read pairs after data processing.

Techniques Used: Mutagenesis, DNA Sequencing, Plasmid Preparation, Produced, Expressing, Construct, Sequencing, Infection, Polymerase Chain Reaction

HIV-2 has a lower mutation frequency and distinct mutation spectrum relative to HIV-1. a Mutation frequency analysis. Mutation frequencies were calculated by dividing the number of mutations by the number of reference bases (mutations + wild-type bases) and are expressed as mutations/bp, or m/bp. Mutation frequencies were determined for HIV-1 and HIV-2, as well as for plasmid controls to assess background error levels. b Transition frequency analysis. Transition frequencies were compared across the five different amplicons subjected to Illumina DNA sequencing. c Mutation spectra analysis. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage of total mutations. Data in all panels represent the mean of three experimental replicates, with error bars indicating the standard deviation. Asterisks denote statistically significant differences between HIV-1 and 2 (* p
Figure Legend Snippet: HIV-2 has a lower mutation frequency and distinct mutation spectrum relative to HIV-1. a Mutation frequency analysis. Mutation frequencies were calculated by dividing the number of mutations by the number of reference bases (mutations + wild-type bases) and are expressed as mutations/bp, or m/bp. Mutation frequencies were determined for HIV-1 and HIV-2, as well as for plasmid controls to assess background error levels. b Transition frequency analysis. Transition frequencies were compared across the five different amplicons subjected to Illumina DNA sequencing. c Mutation spectra analysis. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage of total mutations. Data in all panels represent the mean of three experimental replicates, with error bars indicating the standard deviation. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

Techniques Used: Mutagenesis, Plasmid Preparation, DNA Sequencing, Standard Deviation

Related Articles

Sequencing:

Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation
Article Snippet: .. HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing. ..

Polymerase Chain Reaction:

Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation
Article Snippet: Plasmid error hotspots (i.e. common sites for background errors due to PCR or sequencing) were identified by examining the distribution of mutation frequencies at every individual position for the HIV-1 and HIV-2 plasmid controls. .. HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

Mutagenesis:

Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation
Article Snippet: Plasmid error hotspots (i.e. common sites for background errors due to PCR or sequencing) were identified by examining the distribution of mutation frequencies at every individual position for the HIV-1 and HIV-2 plasmid controls. .. HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

Plasmid Preparation:

Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation
Article Snippet: Plasmid error hotspots were defined as upper outliers within the distribution using the 1.5 × IQR rule. .. HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

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    Illumina Inc hiv 2 primer
    HIV-1 demonstrates higher G-to-A hypermutant frequencies than <t>HIV-2.</t> a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p
    Hiv 2 Primer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiv 2 primer/product/Illumina Inc
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hiv 2 primer - by Bioz Stars, 2020-02
    80/100 stars
      Buy from Supplier

    93
    Illumina Inc hiv 2 integrase
    HIV-1 demonstrates higher G-to-A hypermutant frequencies than <t>HIV-2.</t> a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p
    Hiv 2 Integrase, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiv 2 integrase/product/Illumina Inc
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hiv 2 integrase - by Bioz Stars, 2020-02
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    HIV-1 demonstrates higher G-to-A hypermutant frequencies than HIV-2. a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

    Journal: Retrovirology

    Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

    doi: 10.1186/s12977-015-0180-6

    Figure Lengend Snippet: HIV-1 demonstrates higher G-to-A hypermutant frequencies than HIV-2. a The frequencies of each type of transition hypermutant were compared between HIV-1, HIV-2, and the plasmid controls. For this analysis, hypermutants were defined as read pairs containing two or more mutations of the indicated type within an individual read pair (approximately 120 bp in length). The frequency of hypermutation was then calculated by dividing the number of hypermutant read pairs by all read pairs. b The frequency of G-to-A hypermutation was compared across all five amplicons examined by Illumina DNA sequencing. c The degree of G-to-A hypermutation was analyzed by determining the numbers of G-to-A mutations within hypermutant read pairs. d The dinucleotide context of G-to-A mutations from G-to-A hypermutants was determined and expressed as a percentage of the total. Data in panels a , b , and d represent the mean of three experimental replicates, with error bars representing standard deviation, while data in panel c represent the total (i.e. compiled) data. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

    Article Snippet: HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

    Techniques: Plasmid Preparation, DNA Sequencing, Standard Deviation

    HIV-1 and HIV-2 mutation frequencies and spectra are similar in the absence of G-to-A hypermutation. a Analysis of mutation frequency in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation frequencies were determined either including or excluding G-to-A hypermutants, with the results superimposed. The relative percentage of the total data that can be attributed (or not attributed) to G-to-A hypermutation is indicated within the bars . b Analysis of HIV-1 and HIV-2 mutation spectra in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation spectra were examined after excluding all G-to-A hypermutants. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage. Data in both panels represent the mean of three experimental replicates.

    Journal: Retrovirology

    Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

    doi: 10.1186/s12977-015-0180-6

    Figure Lengend Snippet: HIV-1 and HIV-2 mutation frequencies and spectra are similar in the absence of G-to-A hypermutation. a Analysis of mutation frequency in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation frequencies were determined either including or excluding G-to-A hypermutants, with the results superimposed. The relative percentage of the total data that can be attributed (or not attributed) to G-to-A hypermutation is indicated within the bars . b Analysis of HIV-1 and HIV-2 mutation spectra in the absence of G-to-A hypermutation. HIV-1 and HIV-2 mutation spectra were examined after excluding all G-to-A hypermutants. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage. Data in both panels represent the mean of three experimental replicates.

    Article Snippet: HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

    Techniques: Mutagenesis

    Experimental strategy for investigating HIV-1 and HIV-2 mutagenesis by Illumina DNA sequencing. Vector virus stocks were produced by co-transfecting 293T cells with HIV-1 or HIV-2 Env-deficient vectors and HIV-1 or HIV-2 CXCR4-tropic Env expression constructs. Virus stocks were concentrated, DNase I-treated to reduce plasmid carryover, and titered in U373-MAGI cells. To prepare samples for Illumina sequencing, 1 × 10 6 U373-MAGI cells were infected at an MOI of 1.0, generating approximately 1 × 10 6 proviruses per experimental replicate. This assay represents a single round of viral replication, as producer cells and target cells cannot be re-infected, due to a lack of receptor or Env expression, respectively. Polymerase chain reaction (PCR) of five amplicons (Gag, Vif, HSA, EGFP-1, and EGFP-2) was performed from the proviral DNA. Amplicons from the HIV-1 and HIV-2 proviral DNAs were either identical (HSA, EGFP-1 and 2) or homologous (Gag and Vif) in sequence. The EGFP-1 and EGFP-2 amplicons represent non-overlapping segments of the egfp gene. Sequencing libraries were prepared from the amplicons, pooled in an equimolar fashion to normalize coverage, and subjected to 2 ×150 bp sequencing on the Illumina MiSeq, generating approximately 4.7 million read pairs after data processing.

    Journal: Retrovirology

    Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

    doi: 10.1186/s12977-015-0180-6

    Figure Lengend Snippet: Experimental strategy for investigating HIV-1 and HIV-2 mutagenesis by Illumina DNA sequencing. Vector virus stocks were produced by co-transfecting 293T cells with HIV-1 or HIV-2 Env-deficient vectors and HIV-1 or HIV-2 CXCR4-tropic Env expression constructs. Virus stocks were concentrated, DNase I-treated to reduce plasmid carryover, and titered in U373-MAGI cells. To prepare samples for Illumina sequencing, 1 × 10 6 U373-MAGI cells were infected at an MOI of 1.0, generating approximately 1 × 10 6 proviruses per experimental replicate. This assay represents a single round of viral replication, as producer cells and target cells cannot be re-infected, due to a lack of receptor or Env expression, respectively. Polymerase chain reaction (PCR) of five amplicons (Gag, Vif, HSA, EGFP-1, and EGFP-2) was performed from the proviral DNA. Amplicons from the HIV-1 and HIV-2 proviral DNAs were either identical (HSA, EGFP-1 and 2) or homologous (Gag and Vif) in sequence. The EGFP-1 and EGFP-2 amplicons represent non-overlapping segments of the egfp gene. Sequencing libraries were prepared from the amplicons, pooled in an equimolar fashion to normalize coverage, and subjected to 2 ×150 bp sequencing on the Illumina MiSeq, generating approximately 4.7 million read pairs after data processing.

    Article Snippet: HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

    Techniques: Mutagenesis, DNA Sequencing, Plasmid Preparation, Produced, Expressing, Construct, Sequencing, Infection, Polymerase Chain Reaction

    HIV-2 has a lower mutation frequency and distinct mutation spectrum relative to HIV-1. a Mutation frequency analysis. Mutation frequencies were calculated by dividing the number of mutations by the number of reference bases (mutations + wild-type bases) and are expressed as mutations/bp, or m/bp. Mutation frequencies were determined for HIV-1 and HIV-2, as well as for plasmid controls to assess background error levels. b Transition frequency analysis. Transition frequencies were compared across the five different amplicons subjected to Illumina DNA sequencing. c Mutation spectra analysis. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage of total mutations. Data in all panels represent the mean of three experimental replicates, with error bars indicating the standard deviation. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

    Journal: Retrovirology

    Article Title: HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation

    doi: 10.1186/s12977-015-0180-6

    Figure Lengend Snippet: HIV-2 has a lower mutation frequency and distinct mutation spectrum relative to HIV-1. a Mutation frequency analysis. Mutation frequencies were calculated by dividing the number of mutations by the number of reference bases (mutations + wild-type bases) and are expressed as mutations/bp, or m/bp. Mutation frequencies were determined for HIV-1 and HIV-2, as well as for plasmid controls to assess background error levels. b Transition frequency analysis. Transition frequencies were compared across the five different amplicons subjected to Illumina DNA sequencing. c Mutation spectra analysis. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage of total mutations. Data in all panels represent the mean of three experimental replicates, with error bars indicating the standard deviation. Asterisks denote statistically significant differences between HIV-1 and 2 (* p

    Article Snippet: HIV-1 and HIV-2 primer and barcode sequences for Illumina sequencing.

    Techniques: Mutagenesis, Plasmid Preparation, DNA Sequencing, Standard Deviation