illumina miseq system Search Results


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  • 93
    Thermo Fisher illumina miseq
    Illumina Miseq, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Thermo Fisher
    Average 93 stars, based on 38 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    93/100 stars
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    99
    Illumina Inc illumina miseq illumina
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq Illumina, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1706 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq illumina/product/Illumina Inc
    Average 99 stars, based on 1706 article reviews
    Price from $9.99 to $1999.99
    illumina miseq illumina - by Bioz Stars, 2020-04
    99/100 stars
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    93
    ChunLab illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by ChunLab, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/ChunLab
    Average 93 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    93/100 stars
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    94
    GATC Biotech illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by GATC Biotech, used in various techniques. Bioz Stars score: 94/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/GATC Biotech
    Average 94 stars, based on 36 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    94/100 stars
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    92
    ProteinCT illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by ProteinCT, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/ProteinCT
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    92/100 stars
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    87
    Roche illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Roche, used in various techniques. Bioz Stars score: 87/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Roche
    Average 87 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    87/100 stars
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    92
    Sangon Biotech illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Sangon Biotech
    Average 92 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    92/100 stars
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    94
    3M Co illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by 3M Co, used in various techniques. Bioz Stars score: 94/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/3M Co
    Average 94 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    94/100 stars
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    94
    Novogene illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Novogene, used in various techniques. Bioz Stars score: 94/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Novogene
    Average 94 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    94/100 stars
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    93
    Pacific Biosciences illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Pacific Biosciences
    Average 93 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    93/100 stars
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    95
    Genomed GmbH illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Genomed GmbH, used in various techniques. Bioz Stars score: 95/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Genomed GmbH
    Average 95 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    95/100 stars
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    92
    SciGenom illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by SciGenom, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/SciGenom
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    92/100 stars
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    93
    Macrogen illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by Macrogen, used in various techniques. Bioz Stars score: 93/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/Macrogen
    Average 93 stars, based on 30 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    93/100 stars
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    91
    SeqWright illumina miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq, supplied by SeqWright, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq/product/SeqWright
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    illumina miseq - by Bioz Stars, 2020-04
    91/100 stars
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    96
    Illumina Inc illumina hiseq miseq
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Hiseq Miseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq miseq/product/Illumina Inc
    Average 96 stars, based on 95 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq miseq - by Bioz Stars, 2020-04
    96/100 stars
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    99
    Illumina Inc illumina miseq cartridge
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq Cartridge, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 280 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq cartridge/product/Illumina Inc
    Average 99 stars, based on 280 article reviews
    Price from $9.99 to $1999.99
    illumina miseq cartridge - by Bioz Stars, 2020-04
    99/100 stars
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    94
    Genentech illumina miseq platform
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Illumina Miseq Platform, supplied by Genentech, used in various techniques. Bioz Stars score: 94/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq platform/product/Genentech
    Average 94 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    illumina miseq platform - by Bioz Stars, 2020-04
    94/100 stars
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    94
    Microsynth illumina miseq platform
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
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    Roche illumina miseq platform
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
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    Sangon Biotech illumina miseq 2000
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
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    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
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    Illumina Inc illumina miseq 300
    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the <t>Illumina</t> <t>MiSeq.</t> (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
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    Illumina Inc illumina miseq approach
    Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by <t>Illumina</t> <t>MiSeq</t> sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.
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    Novogen illumina miseq platform
    Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by <t>Illumina</t> <t>MiSeq</t> sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.
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    Novogene illumina miseq platform
    Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by <t>Illumina</t> <t>MiSeq</t> sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.
    Illumina Miseq Platform, supplied by Novogene, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Genomed GmbH illumina miseq pe300
    Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by <t>Illumina</t> <t>MiSeq</t> sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.
    Illumina Miseq Pe300, supplied by Genomed GmbH, used in various techniques. Bioz Stars score: 95/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LGC Genomics GmbH illumina miseq platform
    Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).
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    Microsynth illumina miseq system
    Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).
    Illumina Miseq System, supplied by Microsynth, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LGC Genomics GmbH illumina miseq v3
    Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).
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    Illumina Inc illumina miseq 3000
    Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).
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    Eurofins illumina miseq platform
    Taxonomic composition of Gammaproteobacteria communities inhabiting rhizosphere, endorhiza, pseudostem, and leaves of banana plants from Nicaragua (left) and Costa Rica (right) grown under different agroforestry conditions . Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, family and genus level. Samples were encoded using abbreviations indicating: (1) country (N−, Nicaragua; C−, Costa Rica), (2) microenvironment (S, rhizosphere soil; Re, endorhiza; Ps, pseudostem; L, leaves), (3) farm (1, 2, 3), and (4) agroforestry conditions (T+, with trees; T−, without trees).
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    GATC Biotech illumina miseq platform
    Taxonomic composition of Gammaproteobacteria communities inhabiting rhizosphere, endorhiza, pseudostem, and leaves of banana plants from Nicaragua (left) and Costa Rica (right) grown under different agroforestry conditions . Sequences obtained by <t>Illumina</t> <t>MiSeq</t> sequencing were classified at order, family and genus level. Samples were encoded using abbreviations indicating: (1) country (N−, Nicaragua; C−, Costa Rica), (2) microenvironment (S, rhizosphere soil; Re, endorhiza; Ps, pseudostem; L, leaves), (3) farm (1, 2, 3), and (4) agroforestry conditions (T+, with trees; T−, without trees).
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    Image Search Results


    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the Illumina MiSeq. (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.

    Journal: Retrovirology

    Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq

    doi: 10.1186/s12977-014-0122-8

    Figure Lengend Snippet: Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the Illumina MiSeq. (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.

    Article Snippet: Lastly, Illumina MiSeq is the first and only next-generation sequencing platform to receive FDA approval for assays developed on that device, making it the optimal deep sequencing platform to develop a HIV drug resistance assay for possible clinical use in the future [ ].

    Techniques: Sequencing, Isolation, Reverse Transcription Polymerase Chain Reaction, Amplification, Nested PCR, Polymerase Chain Reaction, Purification, Nucleic Acid Electrophoresis, Gel Extraction, Magnetic Beads, Multiplexing, Concentration Assay, Software

    Laboratory procedure used to obtain MHC II DRB short and long amplicons, and assembly pipelines. The short amplicon was sequenced by standard Sanger sequencing (step 1), while the long amplicon was sequenced with Illumina MiSeq and nanopore MinION after gel extraction (step 2). The gene structure is based on Bos taurus (Ensembl: ENSBTAG00000013919) and Ovis aries (GenBank AM884914) structures. Boxes: coding regions, lines: introns, horizontal arrows: PCR primers

    Journal: Heredity

    Article Title: A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra)

    doi: 10.1038/s41437-018-0070-5

    Figure Lengend Snippet: Laboratory procedure used to obtain MHC II DRB short and long amplicons, and assembly pipelines. The short amplicon was sequenced by standard Sanger sequencing (step 1), while the long amplicon was sequenced with Illumina MiSeq and nanopore MinION after gel extraction (step 2). The gene structure is based on Bos taurus (Ensembl: ENSBTAG00000013919) and Ovis aries (GenBank AM884914) structures. Boxes: coding regions, lines: introns, horizontal arrows: PCR primers

    Article Snippet: De novo assembly of MiSeq Illumina reads The Illumina sequencing of all six libraries produced 1,243,596 paired-end reads.

    Techniques: Amplification, Sequencing, Gel Extraction, Polymerase Chain Reaction

    Annotated OTUs per platform at all taxonomic levels. Percentage (%) of annotated OTUs on each taxonomic level for both Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT) sequencing platforms.

    Journal: Scientific Reports

    Article Title: Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

    doi: 10.1038/s41598-018-23296-4

    Figure Lengend Snippet: Annotated OTUs per platform at all taxonomic levels. Percentage (%) of annotated OTUs on each taxonomic level for both Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT) sequencing platforms.

    Article Snippet: Faecal bacterial communities were profiled by 16S rRNA amplicon sequencing using two NGS platforms: Illumina MiSeq (MiSeq) and Ion Torrent PGM (IT).

    Techniques: Sequencing

    Forward and reverse read quality profiles for 300 cycles on the Illumina HiSeq (1,536 samples) and MiSeq (444 samples) platforms. Amplicon libraries were prepared using a 2-step PCR method. Shown for each cycle are the mean quality score (green line), the median quality score (solid purple line), and the quartiles of the quality score distribution (dotted purple lines).

    Journal: mSystems

    Article Title: Ultrahigh-Throughput Multiplexing and Sequencing of > 500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

    doi: 10.1128/mSystems.00029-19

    Figure Lengend Snippet: Forward and reverse read quality profiles for 300 cycles on the Illumina HiSeq (1,536 samples) and MiSeq (444 samples) platforms. Amplicon libraries were prepared using a 2-step PCR method. Shown for each cycle are the mean quality score (green line), the median quality score (solid purple line), and the quartiles of the quality score distribution (dotted purple lines).

    Article Snippet: Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300-bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform.

    Techniques: Amplification, Polymerase Chain Reaction

    Normalised variants displayed in IGV. IGV display of Illumina MiSeq reads from a clinical patient highlighting the variation in the representation of indels within BAM files. The same variant is represented differently in three sets of reads which need to be merged to a single locus with the standardized HGVS nomenclature of NM_000314.4:c.21_22dup. Additionally, the reads contributing to the three read sets must be combined to calculate the correct variant allele frequency

    Journal: BMC Bioinformatics

    Article Title: Canary: an atomic pipeline for clinical amplicon assays

    doi: 10.1186/s12859-017-1950-z

    Figure Lengend Snippet: Normalised variants displayed in IGV. IGV display of Illumina MiSeq reads from a clinical patient highlighting the variation in the representation of indels within BAM files. The same variant is represented differently in three sets of reads which need to be merged to a single locus with the standardized HGVS nomenclature of NM_000314.4:c.21_22dup. Additionally, the reads contributing to the three read sets must be combined to calculate the correct variant allele frequency

    Article Snippet: The samples were run on an Illumina MiSeq sequencer and the reads converted to paired-end FASTQ files.

    Techniques: Variant Assay

    PR8-induced IFN-Is alter the fecal microbiota composition, Analysis of fecal microbiota in WT and Ifnar1 -/- mice performed by MiSeq and 16S qPCR during influenza infection. A) Experimental model. Fecal samples were collected from mice on day 0 before infection and on day 9 after mock and PR8 infection. Mice were euthanized at 17 dpi. B, C) The fecal microbiota from WT and Ifnar1 -/- mice on day 0 before infection (n = 6 WT, n = 6 Ifnar1 -/- ), and on day 9 after mock (n = 3 WT, n = 3 Ifnar1 -/- ) and PR8 infection (n = 3 WT, n = 3 Ifnar1 -/- ) was analyzed by sequencing using the Illumina MiSeq system. Graphed is the average relative abundance of each bacterial phylum (B) and genus (C); the cut-off abundance level was set at 0.5%. D) Analysis of the fecal Enterobacteriaceae using 16S qPCR. Fecal samples were collected from mice on day 0 before infection (n = 10 WT, n = 8 Ifnar1 -/- ) and on day 9 after mock (n = 5 WT, n = 4 Ifnar1 -/- ) and PR8 infection (n = 5 WT, n = 4 Ifnar1 -/- ). Copy numbers of Enterobacteriaceae per μl of fecal microbial DNA is shown. Each dot represents one mouse, the geometric mean is indicated. P values were calculated by One-Way ANOVA (Bonferroni multiple comparison test). ***p

    Journal: PLoS Pathogens

    Article Title: Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons

    doi: 10.1371/journal.ppat.1005572

    Figure Lengend Snippet: PR8-induced IFN-Is alter the fecal microbiota composition, Analysis of fecal microbiota in WT and Ifnar1 -/- mice performed by MiSeq and 16S qPCR during influenza infection. A) Experimental model. Fecal samples were collected from mice on day 0 before infection and on day 9 after mock and PR8 infection. Mice were euthanized at 17 dpi. B, C) The fecal microbiota from WT and Ifnar1 -/- mice on day 0 before infection (n = 6 WT, n = 6 Ifnar1 -/- ), and on day 9 after mock (n = 3 WT, n = 3 Ifnar1 -/- ) and PR8 infection (n = 3 WT, n = 3 Ifnar1 -/- ) was analyzed by sequencing using the Illumina MiSeq system. Graphed is the average relative abundance of each bacterial phylum (B) and genus (C); the cut-off abundance level was set at 0.5%. D) Analysis of the fecal Enterobacteriaceae using 16S qPCR. Fecal samples were collected from mice on day 0 before infection (n = 10 WT, n = 8 Ifnar1 -/- ) and on day 9 after mock (n = 5 WT, n = 4 Ifnar1 -/- ) and PR8 infection (n = 5 WT, n = 4 Ifnar1 -/- ). Copy numbers of Enterobacteriaceae per μl of fecal microbial DNA is shown. Each dot represents one mouse, the geometric mean is indicated. P values were calculated by One-Way ANOVA (Bonferroni multiple comparison test). ***p

    Article Snippet: Libraries were sequenced using an Illumina MiSeq system.

    Techniques: Mouse Assay, Real-time Polymerase Chain Reaction, Infection, Sequencing

    OTUs of HT-58-2 cultures grown in BG-11 or BG-11o. 16S rRNA V3-V4 regions from a 20-day culture grown in light were amplified and sequenced using Illumina MiSeq. The identity of the binned OTUs was determined by BLASTN and One Codex. The absence of nitrate (BG-11o) slightly alters the distribution of HT-58-2 community bacteria. One Porphyrobacter species comprises 97% of the Erythrobacteraceae OTUs.

    Journal: Applied and Environmental Microbiology

    Article Title: Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community

    doi: 10.1128/AEM.01068-17

    Figure Lengend Snippet: OTUs of HT-58-2 cultures grown in BG-11 or BG-11o. 16S rRNA V3-V4 regions from a 20-day culture grown in light were amplified and sequenced using Illumina MiSeq. The identity of the binned OTUs was determined by BLASTN and One Codex. The absence of nitrate (BG-11o) slightly alters the distribution of HT-58-2 community bacteria. One Porphyrobacter species comprises 97% of the Erythrobacteraceae OTUs.

    Article Snippet: Samples were diluted to 10 nM in 10 mM Tris buffer (pH 8.5) and used for sequencing on an Illumina MiSeq instrument.

    Techniques: Amplification

    Evaluation of the MIRU-profiler on the genome assemblies based on Illumina Miseq reads. (A) A summary of the evaluation results is presented in the boxplot where number of matched, mismatched and indeterminate loci (unknown allele number or not detected) per sample are shown. (B) Percentage agreement between MIRU-profiler and experimental results for each locus is shown. (C) The effect of average sequencing depth on the number of loci that could be detected by the MIRU-profiler is shown. The analysis was performed by down sampling reads from one of the samples to 5×, 10×, 15×, 20×, 25× and 30×.

    Journal: PeerJ

    Article Title: MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis

    doi: 10.7717/peerj.5090

    Figure Lengend Snippet: Evaluation of the MIRU-profiler on the genome assemblies based on Illumina Miseq reads. (A) A summary of the evaluation results is presented in the boxplot where number of matched, mismatched and indeterminate loci (unknown allele number or not detected) per sample are shown. (B) Percentage agreement between MIRU-profiler and experimental results for each locus is shown. (C) The effect of average sequencing depth on the number of loci that could be detected by the MIRU-profiler is shown. The analysis was performed by down sampling reads from one of the samples to 5×, 10×, 15×, 20×, 25× and 30×.

    Article Snippet: The results of the MIRU-profiler evaluation on the genome assemblies based on 250 bp paired-end reads from the Illumina MiSeq machine are detailed in and illustrated in .

    Techniques: Sequencing, Sampling

    Alteration of fecal bacterial communities in Opn KO mice. Eight-week-old female Opn KO and WT mice were co-housed for 3 weeks prior to collection of feces and extraction of DNA. These mice were bred and maintained in the same facility for at least three generations. Illumina MiSeq analysis of 16S rRNA was then performed. Data are from (a) each sample and (b) the average of the groups. Data was normalized against common bacterial 16S rRNA expression and is presented as a ratio to the value obtained in WT mice (n = 5, per group).

    Journal: PLoS ONE

    Article Title: The potential role of Osteopontin in the maintenance of commensal bacteria homeostasis in the intestine

    doi: 10.1371/journal.pone.0173629

    Figure Lengend Snippet: Alteration of fecal bacterial communities in Opn KO mice. Eight-week-old female Opn KO and WT mice were co-housed for 3 weeks prior to collection of feces and extraction of DNA. These mice were bred and maintained in the same facility for at least three generations. Illumina MiSeq analysis of 16S rRNA was then performed. Data are from (a) each sample and (b) the average of the groups. Data was normalized against common bacterial 16S rRNA expression and is presented as a ratio to the value obtained in WT mice (n = 5, per group).

    Article Snippet: To examine whether Opn-producing cells play a role in the homeostasis of commensal microflora, we examined the composition of intestinal bacteria using Illumina MiSeq analysis of DNA extracted from fecal samples collected from co-housed WT and Opn KO mice.

    Techniques: Mouse Assay, Expressing

    The laboratory pipeline for T cell receptor (TCR) sequencing. 1. RNA is extracted from cells or tissues, using standard protocols, quantified and checked for integrity. 2. Residual DNA is removed by DNAse treatment, and TCR RNA is then reverse transcribed into cDNA using primers close to the 5′ end of the constant region. 3. An oligonucleotide containing the Illumina SP2 sequencing primer, and a unique molecular identifier (UMI) consisting of two sets of six random nucleotides separated by spacers as shown, is ligated to the 3′ end of the cDNA using T4 RNA Ligase I. 4. The ligated product is amplified by four rounds of PCR, using nested primers in the alpha and beta C region in combination with the SP2 primer. 5. The product is further amplified and extended to incorporate the SP1 sequencing primer, indices for multiplexing and adaptors as shown. The final purified product is mixed with other indexed samples to give the final library, analyzed by capillary electrophoresis and sequenced on an Illumina MiSeq or Nextseq. PuX indicate the various purification steps.

    Journal: Frontiers in Immunology

    Article Title: Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

    doi: 10.3389/fimmu.2017.01267

    Figure Lengend Snippet: The laboratory pipeline for T cell receptor (TCR) sequencing. 1. RNA is extracted from cells or tissues, using standard protocols, quantified and checked for integrity. 2. Residual DNA is removed by DNAse treatment, and TCR RNA is then reverse transcribed into cDNA using primers close to the 5′ end of the constant region. 3. An oligonucleotide containing the Illumina SP2 sequencing primer, and a unique molecular identifier (UMI) consisting of two sets of six random nucleotides separated by spacers as shown, is ligated to the 3′ end of the cDNA using T4 RNA Ligase I. 4. The ligated product is amplified by four rounds of PCR, using nested primers in the alpha and beta C region in combination with the SP2 primer. 5. The product is further amplified and extended to incorporate the SP1 sequencing primer, indices for multiplexing and adaptors as shown. The final purified product is mixed with other indexed samples to give the final library, analyzed by capillary electrophoresis and sequenced on an Illumina MiSeq or Nextseq. PuX indicate the various purification steps.

    Article Snippet: The final 4 nM library is then prepared for sequencing using the standard Illumina MiSeq protocol.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Multiplexing, Purification, Electrophoresis

    Schematic overview of microbiome bioinformatic analysis workflow. The hypervariable V4 region of 16S rDNA from tick samples was sequenced and split by barcode with Illumina MiSeq. Resulting paired-end reads were joined and the primer region was removed. Reads were filtered by amplicon length and aligned to SILVA as the reference database. After removal of chimeras, reads were clustered into operational taxonomic units (OTU) and taxonomically classified. Finally, an OTU-table was created and results were visualized

    Journal: Parasites & Vectors

    Article Title: Combination of microbiome analysis and serodiagnostics to assess the risk of pathogen transmission by ticks to humans and animals in central Germany

    doi: 10.1186/s13071-018-3240-7

    Figure Lengend Snippet: Schematic overview of microbiome bioinformatic analysis workflow. The hypervariable V4 region of 16S rDNA from tick samples was sequenced and split by barcode with Illumina MiSeq. Resulting paired-end reads were joined and the primer region was removed. Reads were filtered by amplicon length and aligned to SILVA as the reference database. After removal of chimeras, reads were clustered into operational taxonomic units (OTU) and taxonomically classified. Finally, an OTU-table was created and results were visualized

    Article Snippet: All samples were diluted to the same molarity, pooled together, spiked with an internal control (15% PhiX) and paired-end sequenced on the MiSeq Illumina platform using a flow cell with V2 chemistry (500 cycles).

    Techniques: Amplification

    Heatmap of all 97% operational taxonomic units ( OTU s) that had at least 5% relative abundance in one sample of the diet experiment data set generated on the Illumina MiSeq platform. Colours in each cell reveal relative abundances of the identified OTU s within each sample (columns), and cells are not outlined if the OTU s were absent. Sample columns are ordered by species pair, nest ID and treatment group, while OTU s are listed in rows and ordered based on the bacterial phylogenetic tree given towards the left. OTU classifications and the total number of assigned reads per OTU across the 36 samples are given towards the right and are colour‐coded by bacterial order, as shown in the bacterial phylogeny. Asterisks show the OTU s that were consistently shared by hosts and parasites across all treatment groups in a least one nest. Arrow direction highlights the OTU s that substantially increased or decreased between the start of the experiment and the end of the sucrose treatment as shown by the similarity percentages test ( SIMPER ; for complete results see Table S9, Supporting information).

    Journal: Molecular Ecology

    Article Title: Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus‐growing ant hosts

    doi: 10.1111/mec.13216

    Figure Lengend Snippet: Heatmap of all 97% operational taxonomic units ( OTU s) that had at least 5% relative abundance in one sample of the diet experiment data set generated on the Illumina MiSeq platform. Colours in each cell reveal relative abundances of the identified OTU s within each sample (columns), and cells are not outlined if the OTU s were absent. Sample columns are ordered by species pair, nest ID and treatment group, while OTU s are listed in rows and ordered based on the bacterial phylogenetic tree given towards the left. OTU classifications and the total number of assigned reads per OTU across the 36 samples are given towards the right and are colour‐coded by bacterial order, as shown in the bacterial phylogeny. Asterisks show the OTU s that were consistently shared by hosts and parasites across all treatment groups in a least one nest. Arrow direction highlights the OTU s that substantially increased or decreased between the start of the experiment and the end of the sucrose treatment as shown by the similarity percentages test ( SIMPER ; for complete results see Table S9, Supporting information).

    Article Snippet: H.L. and S.J.S. performed sequencing runs on the Roche Life Sciences 454 GS FLX Titanium and MiSeq Illumina platforms.

    Techniques: Generated

    Phylum‐level distributions of bacterial community, determined by Illumina MiSeq sequencing of bee bread from 20 hives, organized by location (on an east–west axis left to right)

    Journal: Ecology and Evolution

    Article Title: Bacterial communities associated with honeybee food stores are correlated with land use. Bacterial communities associated with honeybee food stores are correlated with land use

    doi: 10.1002/ece3.3999

    Figure Lengend Snippet: Phylum‐level distributions of bacterial community, determined by Illumina MiSeq sequencing of bee bread from 20 hives, organized by location (on an east–west axis left to right)

    Article Snippet: A subset ( n = 48) from 19 hives within 19 apiary sites were used in DNA sequencing with Illumina MiSeq due to constraints in the scope of this and a previous study (See Section , Table ).

    Techniques: Sequencing

    Fecal microbiota composition of healthy, normal weight Chilean subjects by sequencing the V3–V4 of 16S rRNA gene using the MiSeq Illumina system. Relative abundance (%) of phyla (A) and families (B) identified in healthy normal weight Chileans ( n = 41).

    Journal: Frontiers in Microbiology

    Article Title: The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

    doi: 10.3389/fmicb.2017.01221

    Figure Lengend Snippet: Fecal microbiota composition of healthy, normal weight Chilean subjects by sequencing the V3–V4 of 16S rRNA gene using the MiSeq Illumina system. Relative abundance (%) of phyla (A) and families (B) identified in healthy normal weight Chileans ( n = 41).

    Article Snippet: The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system.

    Techniques: Sequencing

    H3K9ac ChIP-seq on SOLiD 5500xl vs. Illumina MiSeq. (A) Representative UCSC genome browser screenshots from H3K9ac ChIP-DNA sequenced on a SOLiD 5500xl (blue tracks) and an Illumina MiSeq (orange tracks). Note enrichment of ChIP-DNA tracks over input controls (gray tracks). Light blue boxes indicate gaps in the SOLiD 5500xl sequencing tracks, as compared with the Illumina sequencing tracks, typically, over CpG islands (green bars). (B) (Left) graph shows genomic elements with occupancy with the H3K9ac mark, plotted with corresponding number of peaks. (Right) dotted grid displays distribution of peaks over these genomic elements, including the information if peaks cover multiple genomic elements. (C) (Left side of the panel) Cartoon of experimental design for H3K9ac ChIP-seq with ePCR in 80 mL and 20 mL pouches (SOLiD) and with bridge PCR (Illumina). (Right side of the panel) Box-plots show sequencing coverage for H3K9ac on the SOLiD 5500xl (20 mL pouch, cyan and 80 mL pouch, blue) and on an Illumina platform (MiSeq, orange) for promoters, exons, introns, 3′UTRs, and 5′UTRs. (D) CpG island plots showcase coverage for the island and its shores, continuously 2kb up and downstream from the CpG island. Coverage is expressed in reads per million (RPM).

    Journal: Nucleus

    Article Title: Sequencing on the SOLiD 5500xl System – in-depth characterization of the GC bias

    doi: 10.1080/19491034.2017.1320461

    Figure Lengend Snippet: H3K9ac ChIP-seq on SOLiD 5500xl vs. Illumina MiSeq. (A) Representative UCSC genome browser screenshots from H3K9ac ChIP-DNA sequenced on a SOLiD 5500xl (blue tracks) and an Illumina MiSeq (orange tracks). Note enrichment of ChIP-DNA tracks over input controls (gray tracks). Light blue boxes indicate gaps in the SOLiD 5500xl sequencing tracks, as compared with the Illumina sequencing tracks, typically, over CpG islands (green bars). (B) (Left) graph shows genomic elements with occupancy with the H3K9ac mark, plotted with corresponding number of peaks. (Right) dotted grid displays distribution of peaks over these genomic elements, including the information if peaks cover multiple genomic elements. (C) (Left side of the panel) Cartoon of experimental design for H3K9ac ChIP-seq with ePCR in 80 mL and 20 mL pouches (SOLiD) and with bridge PCR (Illumina). (Right side of the panel) Box-plots show sequencing coverage for H3K9ac on the SOLiD 5500xl (20 mL pouch, cyan and 80 mL pouch, blue) and on an Illumina platform (MiSeq, orange) for promoters, exons, introns, 3′UTRs, and 5′UTRs. (D) CpG island plots showcase coverage for the island and its shores, continuously 2kb up and downstream from the CpG island. Coverage is expressed in reads per million (RPM).

    Article Snippet: The peaks with the loss of coverage on the SOLiD sequencer were much better preserved when sequenced with the Illumina system MiSeq ( and , orange tracks).

    Techniques: Chromatin Immunoprecipitation, Sequencing, Bridge PCR

    Comparison of the different methylation quantifying methods. Each marker was analyzed in one sample of the target fluid by bisulfite sequencing, SNaPshot reaction, Roche 454 and Illumina MiSeq NGS respectively.

    Journal: PLoS ONE

    Article Title: Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence

    doi: 10.1371/journal.pone.0147973

    Figure Lengend Snippet: Comparison of the different methylation quantifying methods. Each marker was analyzed in one sample of the target fluid by bisulfite sequencing, SNaPshot reaction, Roche 454 and Illumina MiSeq NGS respectively.

    Article Snippet: Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals.

    Techniques: Methylation, Marker, Methylation Sequencing, Next-Generation Sequencing

    Correctly classified reads for all 16S rRNA gene regions at different taxonomic levels using the ( A ) SILVA and ( B ) NCBI 16S databases for Illumina MiSeq data. Percentages are expressed against the total number of reads classified at any taxonomic level (SILVA only allows classification until the genus).

    Journal: International Journal of Molecular Sciences

    Article Title: Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies

    doi: 10.3390/ijms21010298

    Figure Lengend Snippet: Correctly classified reads for all 16S rRNA gene regions at different taxonomic levels using the ( A ) SILVA and ( B ) NCBI 16S databases for Illumina MiSeq data. Percentages are expressed against the total number of reads classified at any taxonomic level (SILVA only allows classification until the genus).

    Article Snippet: Generation and Analysis of Sequencing Data for Different 16S rRNA Gene Regions with the Illumina (MiSeq) Technology

    Techniques:

    Community structure and taxonomic affiliation of nirS -type denitrifiers in the groundwater of the two aquifer assemblages based on Illumina MiSeq amplicon sequencing of nirS genes, August 2014. Sequences showing less than 80% nirS sequence identity with cultured denitrifiers were referred to as “unclassified.”

    Journal: Frontiers in Microbiology

    Article Title: Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

    doi: 10.3389/fmicb.2017.01951

    Figure Lengend Snippet: Community structure and taxonomic affiliation of nirS -type denitrifiers in the groundwater of the two aquifer assemblages based on Illumina MiSeq amplicon sequencing of nirS genes, August 2014. Sequences showing less than 80% nirS sequence identity with cultured denitrifiers were referred to as “unclassified.”

    Article Snippet: Because of insufficient amplification of nirK genes for MiSeq Illumina sequencing at very low nirK gene abundances in the groundwater, a detailed analysis of denitrifier community composition focused on nirS -type denitrifiers only. nirS sequences were analyzed using Mothur with few modifications necessary to adjust the pipeline for the analysis of protein-encoding genes, integrating BioEdit (Hall, ), and the ARB package (Ludwig et al., ).

    Techniques: Amplification, Sequencing, Cell Culture

    Structure of the total bacterial community (A) and of the anammox bacterial community (B) based on MiSeq Illumina amplicon sequencing of 16S rRNA genes in the groundwater of seven wells across the two aquifer assemblages, analysis based on metagenomic DNA [August (A) and November (N) 2015]. For (B) Bars represent fractions of sequences assigned to different Candidatus genera of anammox bacteria within the Brocadiaceae (corresponding to 39 up to 4,264 sequence reads out of 16,383 total bacterial 16S rRNA sequence reads per well).

    Journal: Frontiers in Microbiology

    Article Title: Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

    doi: 10.3389/fmicb.2017.01951

    Figure Lengend Snippet: Structure of the total bacterial community (A) and of the anammox bacterial community (B) based on MiSeq Illumina amplicon sequencing of 16S rRNA genes in the groundwater of seven wells across the two aquifer assemblages, analysis based on metagenomic DNA [August (A) and November (N) 2015]. For (B) Bars represent fractions of sequences assigned to different Candidatus genera of anammox bacteria within the Brocadiaceae (corresponding to 39 up to 4,264 sequence reads out of 16,383 total bacterial 16S rRNA sequence reads per well).

    Article Snippet: Because of insufficient amplification of nirK genes for MiSeq Illumina sequencing at very low nirK gene abundances in the groundwater, a detailed analysis of denitrifier community composition focused on nirS -type denitrifiers only. nirS sequences were analyzed using Mothur with few modifications necessary to adjust the pipeline for the analysis of protein-encoding genes, integrating BioEdit (Hall, ), and the ARB package (Ludwig et al., ).

    Techniques: Amplification, Sequencing

    Error rate of amplification and deep sequencing for each NGS platform at each position of the V3 sequence. The error rates for the MiSeq Illumina (Fig. 1A) and 454 GS-Junior (Fig. 1B) are shown on two separate graphs. The global mean (blue line) is the mean frequency of artifactual V3 variants of 20 virus clones. The position mean (red line) is the error rate estimated at each position of V3 by comparing the UDS reads to the Sanger sequences of 20 clones. The shaded regions represent the 99% confidence interval of global (blue) and position (red) mean error rates.

    Journal: Scientific Reports

    Article Title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use

    doi: 10.1038/srep42215

    Figure Lengend Snippet: Error rate of amplification and deep sequencing for each NGS platform at each position of the V3 sequence. The error rates for the MiSeq Illumina (Fig. 1A) and 454 GS-Junior (Fig. 1B) are shown on two separate graphs. The global mean (blue line) is the mean frequency of artifactual V3 variants of 20 virus clones. The position mean (red line) is the error rate estimated at each position of V3 by comparing the UDS reads to the Sanger sequences of 20 clones. The shaded regions represent the 99% confidence interval of global (blue) and position (red) mean error rates.

    Article Snippet: We have demonstrated that the MiSeq Illumina technology is as accurate as the 454 GS-Junior Roche system technology for determining HIV-1 tropism compared to a reference phenotypic assay.

    Techniques: Amplification, Sequencing, Next-Generation Sequencing, Clone Assay

    Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by Illumina MiSeq sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.

    Journal: PLoS ONE

    Article Title: PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

    doi: 10.1371/journal.pone.0116264

    Figure Lengend Snippet: Phylogenetic positions of fungal endo-β-1,4-xylanase (GH11) amino-acid sequences. Fungal GH11 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by Illumina MiSeq sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.

    Article Snippet: We then evaluated the suitability of several of the resulting PCR products for high-throughput sequencing using the Illumina MiSeq approach.

    Techniques: Amplification, Sequencing

    Distribution of the Illumina MiSeq sequences within the 20 first most abundant GH11 (A), GH7 (B) and AA2 (C) sequence clusters. Nucleotide sequences obtained from the two studied forest soils collected in 2010 under spruce (BS2010) and beech (BB2010) were clustered at 95 (GH11 and GH7) or 93% (AA2) identity threshold.

    Journal: PLoS ONE

    Article Title: PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

    doi: 10.1371/journal.pone.0116264

    Figure Lengend Snippet: Distribution of the Illumina MiSeq sequences within the 20 first most abundant GH11 (A), GH7 (B) and AA2 (C) sequence clusters. Nucleotide sequences obtained from the two studied forest soils collected in 2010 under spruce (BS2010) and beech (BB2010) were clustered at 95 (GH11 and GH7) or 93% (AA2) identity threshold.

    Article Snippet: We then evaluated the suitability of several of the resulting PCR products for high-throughput sequencing using the Illumina MiSeq approach.

    Techniques: Sequencing

    Phylogenetic positions of Basidiomycota class II peroxidase (AA2) amino-acid sequences. Basidiomycota AA2 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by Illumina MiSeq sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.

    Journal: PLoS ONE

    Article Title: PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

    doi: 10.1371/journal.pone.0116264

    Figure Lengend Snippet: Phylogenetic positions of Basidiomycota class II peroxidase (AA2) amino-acid sequences. Basidiomycota AA2 amino-acid sequences were deduced from the nucleotide sequences amplified from beech (BB) or spruce (BS) soil cDNAs. The Maximum-likelihood phylogenetic tree includes all Sanger sequences amplified from the 2007 soil cDNA samples (BS2007 and BB2007) and all non-singleton sequence clusters detected by Illumina MiSeq sequencing of the 2010 soil cDNA samples (BS2010 and BB2010). Representative Ascomycota and Basidiomycota sequences are marked in red and blue, respectively, whereas the environmental sequences appear in green. Stars identify reference sequences obtained in the present study. Robustness of the tree topology was tested by bootstrap analysis (1000 replicates) and only bootstrap values ≥80 are given.

    Article Snippet: We then evaluated the suitability of several of the resulting PCR products for high-throughput sequencing using the Illumina MiSeq approach.

    Techniques: Amplification, Sequencing

    Beta-diversity analyses of microbial taxa recovered from ATM keypads. Data represent results of unweighted Unifrac PCoAs for 16S rRNA for bacteria/archaea (A to C) and 18S rRNA for eukaryotes (D to F), showing no obvious clustering of microbial assemblages according to NYC neighborhood (A and D), census population demographics (race group with highest proportion in each neighborhood) (B and E), or type of site where ATM was located (F). The strongest clustering pattern in the data set was a technical artifact observed for 16S rRNA samples sequenced across two Illumina MiSeq runs (C).

    Journal: mSphere

    Article Title: Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City

    doi: 10.1128/mSphere.00226-16

    Figure Lengend Snippet: Beta-diversity analyses of microbial taxa recovered from ATM keypads. Data represent results of unweighted Unifrac PCoAs for 16S rRNA for bacteria/archaea (A to C) and 18S rRNA for eukaryotes (D to F), showing no obvious clustering of microbial assemblages according to NYC neighborhood (A and D), census population demographics (race group with highest proportion in each neighborhood) (B and E), or type of site where ATM was located (F). The strongest clustering pattern in the data set was a technical artifact observed for 16S rRNA samples sequenced across two Illumina MiSeq runs (C).

    Article Snippet: During analysis, the strongest clustering pattern observed in our data set was a putative technical artifact resulting from 16S rRNA samples being split across two Illumina MiSeq runs ( ).

    Techniques:

    a Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Bray-Curtis distances. b Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Unweighted UniFrac distances. Lines connect paired sample sequences on the Roche454 ( white tip of line ) and Illumina Miseq ( red tip of line )

    Journal: BMC Microbiology

    Article Title: Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform

    doi: 10.1186/s12866-017-0927-4

    Figure Lengend Snippet: a Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Bray-Curtis distances. b Comparison of beta diversity results for the mock bacterial community and the healthy volunteer skin samples sequenced on both Roche 454 and Illumina MiSeq using Procrustes plot comparing the principal co-ordinates of Unweighted UniFrac distances. Lines connect paired sample sequences on the Roche454 ( white tip of line ) and Illumina Miseq ( red tip of line )

    Article Snippet: The mock bacterial community had an SW diversity index (n = 4 for each platform) of 1.85 and 2 for the Roche 454 Junior and the Illumina MiSeq platforms, respectively, when calculated based on the genus level distribution (Fig.

    Techniques:

    Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by Illumina MiSeq sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).

    Journal: Scientific Reports

    Article Title: Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure

    doi: 10.1038/srep18078

    Figure Lengend Snippet: Taxonomic composition of the gammaproteobacterial communities inhabiting rhizosphere soil (S) and pseudostem (P) of banana plants with and without genetic modifications. Sequences obtained by Illumina MiSeq sequencing were classified at order, familiy and genus level. From each genetic modification, four independent replicate samples were investigated in comparison to non-modified control plants. Sample abbreviations indicate: (1) microenvironment (S = rhizosphere soil, P = pseudostem), (2) breeding line (1, 2), (3) genetic modification, if any (1 = hrap , 2 = pflp ), and (4) independent replicate sample (1–4).

    Article Snippet: Amplicon libraries were generated and sequenced by a paired-end approach using the Illumina MiSeq platform (LGC Genomics, Berlin, Germany).

    Techniques: Sequencing, Modification

    Taxonomic composition of Gammaproteobacteria communities inhabiting rhizosphere, endorhiza, pseudostem, and leaves of banana plants from Nicaragua (left) and Costa Rica (right) grown under different agroforestry conditions . Sequences obtained by Illumina MiSeq sequencing were classified at order, family and genus level. Samples were encoded using abbreviations indicating: (1) country (N−, Nicaragua; C−, Costa Rica), (2) microenvironment (S, rhizosphere soil; Re, endorhiza; Ps, pseudostem; L, leaves), (3) farm (1, 2, 3), and (4) agroforestry conditions (T+, with trees; T−, without trees).

    Journal: Frontiers in Microbiology

    Article Title: Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America

    doi: 10.3389/fmicb.2015.00091

    Figure Lengend Snippet: Taxonomic composition of Gammaproteobacteria communities inhabiting rhizosphere, endorhiza, pseudostem, and leaves of banana plants from Nicaragua (left) and Costa Rica (right) grown under different agroforestry conditions . Sequences obtained by Illumina MiSeq sequencing were classified at order, family and genus level. Samples were encoded using abbreviations indicating: (1) country (N−, Nicaragua; C−, Costa Rica), (2) microenvironment (S, rhizosphere soil; Re, endorhiza; Ps, pseudostem; L, leaves), (3) farm (1, 2, 3), and (4) agroforestry conditions (T+, with trees; T−, without trees).

    Article Snippet: Sequence libraries were generated by a paired-end approach using the Illumina MiSeq platform (Eurofins MWG, Ebersberg, Germany).

    Techniques: Sequencing