amplicons Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Eurofins amplicons
    Rarefaction analysis of the <t>amplicons</t> obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.
    Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 99/100, based on 816 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Eurofins
    Average 99 stars, based on 816 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    93
    MWG-Biotech amplicons
    Rarefaction analysis of the <t>amplicons</t> obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.
    Amplicons, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 93/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/MWG-Biotech
    Average 93 stars, based on 87 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    93/100 stars
      Buy from Supplier

    99
    Illumina Inc amplicons
    Organization of fungal rDNA locus and regions targeted by oligonucleotide probe and primers. Primers UNI1, UNI2, and Cspecies, and probe are used in the qPCR strategy. Primers Fseq and Rseq are used to generate <t>amplicons</t> for sequencing. Cgla, C . glabrata ; Ctro, C . tropicalis ; Cpar, C . parapsilosis ; Ckru, C . krusei ; Calb, C . albicans . Locus depiction is not to scale. Primer sequences are given in Table 1 .
    Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 13970 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Illumina Inc
    Average 99 stars, based on 13970 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    96
    LGC Genomics GmbH amplicons
    Representative image of an agarose gel electrophoresis for the <t>amplicons</t> COI-lf and 16S-sf ( 1 = A. brevispinosa 37,334 A2, 2 = A. brevispinosa 37,334 A1, 3 = A. arbustorum 86,813 A2, 4 = A. arbustorum 100,810 A1, 5 = D. polymorpha 101,850, 6 = D. polymorpha 83,846 B1, 7 = H. pomatia 74,402 B2, 8 = P. planorbis 84,060 A2, C = Negative control)
    Amplicons, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 96/100, based on 188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/LGC Genomics GmbH
    Average 96 stars, based on 188 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    96/100 stars
      Buy from Supplier

    99
    Roche amplicons
    Human defensin gene clusters at 8p23.1 (NCBI build 36, hg18) and location of the <t>amplicons</t> analyzed by 454 (F1-8) and cloning/Sanger (S1-2) sequencing within the proximal DEFB (DEF cluster b2) .
    Amplicons, supplied by Roche, used in various techniques. Bioz Stars score: 99/100, based on 5188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Roche
    Average 99 stars, based on 5188 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher amplicons
    rb1 mutant alleles and allele frequencies in somatic, germline, and tumor tissues from adult genetic mosaic zebrafish. ( a ) 14 different indel alleles in rb1 exon 2 were identified in retina, muscle, and germline genomic DNA from two adults. Mutant alleles represented 33% of cloned <t>amplicons.</t> In tumor tissue 8 unique alleles were identified, representing 87% of cloned amplicons. ( b ) Two frameshift alleles that delete 11 bp and 19 bp in rb1 exon 3 were detected in two adults. 10% of sequenced clones were mutant in retina, muscle or germline tissue. In tumor tissue 68% of sequenced clones were mutant alleles. Red arrows mark TALEN cut site.
    Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 38330 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Thermo Fisher
    Average 99 stars, based on 38330 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    97
    Advanced Analytical Inc amplicons
    rb1 mutant alleles and allele frequencies in somatic, germline, and tumor tissues from adult genetic mosaic zebrafish. ( a ) 14 different indel alleles in rb1 exon 2 were identified in retina, muscle, and germline genomic DNA from two adults. Mutant alleles represented 33% of cloned <t>amplicons.</t> In tumor tissue 8 unique alleles were identified, representing 87% of cloned amplicons. ( b ) Two frameshift alleles that delete 11 bp and 19 bp in rb1 exon 3 were detected in two adults. 10% of sequenced clones were mutant in retina, muscle or germline tissue. In tumor tissue 68% of sequenced clones were mutant alleles. Red arrows mark TALEN cut site.
    Amplicons, supplied by Advanced Analytical Inc, used in various techniques. Bioz Stars score: 97/100, based on 175 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Advanced Analytical Inc
    Average 97 stars, based on 175 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    97/100 stars
      Buy from Supplier

    99
    Macrogen amplicons
    Induction of HCV escape from a direct acting antiviral in HFBR. ( a ) Timeline of Huh7.5 cell cultivation in DMEM + 10%FBS and serum-free AEM, indicating infection with HCV and initiation of treatment with different concentrations of the NS5A inhibitor daclatasvir (DCV). HCV from HFBR harvests (1000 μL, 50 μL or 5 μL) were used for infection of 10 6 Huh7.5 cells plated the previous day in T25 cell culture flasks (derived cultures). Peak infectivity titers in derived cultures are reported. Amino acid at NS5A position 93 according to the H77 reference sequence (GenBank accession no AF009606) was determined by Sanger sequencing for selected harvests and derived cultures. *, H at position 93 was present in ~50% of viral genomes. ( b ) 8 × 10 7 Huh7.5 cells were seeded in a hollow fiber bioreactor in DMEM + 10% FBS and infected with 1.25 × 10 6 FFU of HCV third passage stock on day 5 post cell seeding, when glucose consumption was 590 mg/day (arrow). At day 9 post cell seeding DMEM was replaced with serum-free AEM. Treatment with daclatasvir at 7.8 nM (corresponding to 64 x EC50 29 ) was initiated at day 27 post cell seeding; at day 45 the concentration was increased to 124.2 nM (corresponding to 1024 x EC50). On day 59 the treatment was terminated. ( c and d ) Determination of HCV infectivity titers and HCV RNA titers were carried out as described in Fig. 2 . *, indicates HCV infectivity titers below assay detection level. ( e ) HCV from harvest 9, 12 and 16 were loaded on 10–40% iodixanol gradients. Following ultracentrifugation 18 fractions were collected as in Fig. 5 . HCV infectivity and HCV RNA titers of each fraction were determined as described for Fig. 2 . ( f ) RNA extracted from harvest 9, 12 and 14 at 1-, 10-, 100- and 1000-fold dilution was used for RT-PCR for generation of a full-length amplicon spanning the complete HCV ORF. PCR products were visualized on a 1% agarose gel including a 1 kb DNA ladder; expected positions of full-length <t>amplicons</t> are indicated by arrows. Gel image was cropped as indicated by boxes; full-length gel is presented in Supplementary Fig. S4 .
    Amplicons, supplied by Macrogen, used in various techniques. Bioz Stars score: 99/100, based on 1569 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Macrogen
    Average 99 stars, based on 1569 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    88
    Mirus Bio amplicons
    Analytic detection limits of chemically and enzymatically labeled <t>amplicons.</t> The amplicons were serially diluted and hybridized for 1.5 h at 53°C. The error bars represent the standard deviation. The samples were run in duplicate, and the experiments
    Amplicons, supplied by Mirus Bio, used in various techniques. Bioz Stars score: 88/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Mirus Bio
    Average 88 stars, based on 51 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    88/100 stars
      Buy from Supplier

    99
    Pacific Biosciences amplicons
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 99/100, based on 566 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Pacific Biosciences
    Average 99 stars, based on 566 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    92
    Thermo Fisher 77bp amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    77bp Amplicon, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/77bp amplicon/product/Thermo Fisher
    Average 92 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    77bp amplicon - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    88
    Roche flt3 amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Flt3 Amplicon, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/flt3 amplicon/product/Roche
    Average 88 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    flt3 amplicon - by Bioz Stars, 2020-04
    88/100 stars
      Buy from Supplier

    94
    Illumina Inc truseq amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Truseq Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq amplicon/product/Illumina Inc
    Average 94 stars, based on 61 article reviews
    Price from $9.99 to $1999.99
    truseq amplicon - by Bioz Stars, 2020-04
    94/100 stars
      Buy from Supplier

    86
    Roche amplicon a kit
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon A Kit, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon a kit/product/Roche
    Average 86 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    amplicon a kit - by Bioz Stars, 2020-04
    86/100 stars
      Buy from Supplier

    86
    Sigma-Genosys cygb amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Cygb Amplicon, supplied by Sigma-Genosys, used in various techniques. Bioz Stars score: 86/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cygb amplicon/product/Sigma-Genosys
    Average 86 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    cygb amplicon - by Bioz Stars, 2020-04
    86/100 stars
      Buy from Supplier

    92
    Thermo Fisher v6 amplicons
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    V6 Amplicons, supplied by Thermo Fisher, 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/v6 amplicons/product/Thermo Fisher
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    v6 amplicons - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    95
    Illumina Inc 16s amplicons
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    16s Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 136 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s amplicons/product/Illumina Inc
    Average 95 stars, based on 136 article reviews
    Price from $9.99 to $1999.99
    16s amplicons - by Bioz Stars, 2020-04
    95/100 stars
      Buy from Supplier

    92
    Bio-Rad amplicon detection
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon Detection, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 92/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon detection/product/Bio-Rad
    Average 92 stars, based on 89 article reviews
    Price from $9.99 to $1999.99
    amplicon detection - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    86
    Thermo Fisher amplicon primers
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon Primers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon primers/product/Thermo Fisher
    Average 86 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    amplicon primers - by Bioz Stars, 2020-04
    86/100 stars
      Buy from Supplier

    85
    SAS institute unique amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Unique Amplicon, supplied by SAS institute, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/unique amplicon/product/SAS institute
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    unique amplicon - by Bioz Stars, 2020-04
    85/100 stars
      Buy from Supplier

    92
    Avantor amplicon taq
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon Taq, supplied by Avantor, used in various techniques. Bioz Stars score: 92/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon taq/product/Avantor
    Average 92 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    amplicon taq - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    92
    Millipore 100kda amplicon
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    100kda Amplicon, supplied by Millipore, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100kda amplicon/product/Millipore
    Average 92 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    100kda amplicon - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    85
    Millipore amplicon filters
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon Filters, supplied by Millipore, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon filters/product/Millipore
    Average 85 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    amplicon filters - by Bioz Stars, 2020-04
    85/100 stars
      Buy from Supplier

    93
    Genewiz amplicon identity
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicon Identity, supplied by Genewiz, used in various techniques. Bioz Stars score: 93/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon identity/product/Genewiz
    Average 93 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    amplicon identity - by Bioz Stars, 2020-04
    93/100 stars
      Buy from Supplier

    87
    SABiosciences single amplicons
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Single Amplicons, supplied by SABiosciences, used in various techniques. Bioz Stars score: 87/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/single amplicons/product/SABiosciences
    Average 87 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    single amplicons - by Bioz Stars, 2020-04
    87/100 stars
      Buy from Supplier

    95
    Illumina Inc amplicon data
    Canary read alignment. Overlapping <t>amplicon</t> reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants
    Amplicon Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon data/product/Illumina Inc
    Average 95 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    amplicon data - by Bioz Stars, 2020-04
    95/100 stars
      Buy from Supplier

    86
    Kaneka Corp control amplicon
    Canary read alignment. Overlapping <t>amplicon</t> reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants
    Control Amplicon, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 86/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/control amplicon/product/Kaneka Corp
    Average 86 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    control amplicon - by Bioz Stars, 2020-04
    86/100 stars
      Buy from Supplier

    88
    Bioneer Corporation rassf1a amplicons
    Canary read alignment. Overlapping <t>amplicon</t> reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants
    Rassf1a Amplicons, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rassf1a amplicons/product/Bioneer Corporation
    Average 88 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    rassf1a amplicons - by Bioz Stars, 2020-04
    88/100 stars
      Buy from Supplier

    92
    Illumina Inc truseqcustom amplicon
    Canary read alignment. Overlapping <t>amplicon</t> reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants
    Truseqcustom Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseqcustom amplicon/product/Illumina Inc
    Average 92 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    truseqcustom amplicon - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    99
    Illumina Inc amplicon sequencing
    Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by <t>amplicon</t> sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.
    Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1976 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon sequencing/product/Illumina Inc
    Average 99 stars, based on 1976 article reviews
    Price from $9.99 to $1999.99
    amplicon sequencing - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    92
    Roche amplicon variant analyzer
    Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by <t>amplicon</t> sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.
    Amplicon Variant Analyzer, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon variant analyzer/product/Roche
    Average 92 stars, based on 160 article reviews
    Price from $9.99 to $1999.99
    amplicon variant analyzer - by Bioz Stars, 2020-04
    92/100 stars
      Buy from Supplier

    99
    Thermo Fisher pcr amplicons
    Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by <t>amplicon</t> sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.
    Pcr Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 8656 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr amplicons/product/Thermo Fisher
    Average 99 stars, based on 8656 article reviews
    Price from $9.99 to $1999.99
    pcr amplicons - by Bioz Stars, 2020-04
    99/100 stars
      Buy from Supplier

    Image Search Results


    Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.

    Journal: MicrobiologyOpen

    Article Title: Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river

    doi: 10.1002/mbo3.80

    Figure Lengend Snippet: Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.

    Article Snippet: Amplicons were then subjected to pyrosequencing using a Genome Sequencer 454 Titanium GS FLX (Eurofins, MWG/Operon, Germany).

    Techniques:

    Organization of fungal rDNA locus and regions targeted by oligonucleotide probe and primers. Primers UNI1, UNI2, and Cspecies, and probe are used in the qPCR strategy. Primers Fseq and Rseq are used to generate amplicons for sequencing. Cgla, C . glabrata ; Ctro, C . tropicalis ; Cpar, C . parapsilosis ; Ckru, C . krusei ; Calb, C . albicans . Locus depiction is not to scale. Primer sequences are given in Table 1 .

    Journal: PLoS ONE

    Article Title: Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans

    doi: 10.1371/journal.pone.0116705

    Figure Lengend Snippet: Organization of fungal rDNA locus and regions targeted by oligonucleotide probe and primers. Primers UNI1, UNI2, and Cspecies, and probe are used in the qPCR strategy. Primers Fseq and Rseq are used to generate amplicons for sequencing. Cgla, C . glabrata ; Ctro, C . tropicalis ; Cpar, C . parapsilosis ; Ckru, C . krusei ; Calb, C . albicans . Locus depiction is not to scale. Primer sequences are given in Table 1 .

    Article Snippet: Equal concentrations of amplicons from each individual fecal sample were pooled into a final solution and submitted for Illumina library construction using the TruSeq Nano kit (Illumina, San Diego, CA) and sequencing on an Illumina MiSeq high-throughput sequencing platform using the 2 × 150 bp paired-end version 2 MiSeq Reagent Kit (Illumina) by the University of Minnesota Genomics Center.

    Techniques: Real-time Polymerase Chain Reaction, Sequencing

    EBNA2 position-specific variant frequency observed in sampled healthy donors and individuals with MS Upper and lower panels report individual EBNA2 variant frequencies detected in healthy donor and multiple sclerosis (MS) samples, respectively, through the Illumina MiSeq amplicon sequencing (negative values are used for MS variants). Each dot indicates the individual-specific frequency of a variant at a given EBNA2 position, colored according to a heat map. Positions shared among different individuals are displayed by multiple dots in the same position.

    Journal: Neurology

    Article Title: Epstein-Barr virus genetic variants are associated with multiple sclerosis

    doi: 10.1212/WNL.0000000000001420

    Figure Lengend Snippet: EBNA2 position-specific variant frequency observed in sampled healthy donors and individuals with MS Upper and lower panels report individual EBNA2 variant frequencies detected in healthy donor and multiple sclerosis (MS) samples, respectively, through the Illumina MiSeq amplicon sequencing (negative values are used for MS variants). Each dot indicates the individual-specific frequency of a variant at a given EBNA2 position, colored according to a heat map. Positions shared among different individuals are displayed by multiple dots in the same position.

    Article Snippet: We generated amplicon sequences of the EBNA2 gene from 17 patients and 17 HDs (analyzing one sample for each subject) through the Illumina MiSeq platform from template DNA obtained using a multistep PCR and the Illumina Nextera strategy (Illumina, Inc., San Diego, CA).

    Techniques: Variant Assay, Mass Spectrometry, Amplification, Sequencing

    Representative radiologic and pathologic images of patients with brain somatic mutations in SLC35A2 (A) Preoperative and postoperative brain MRI T2-weighted images from patients EPI219 and LGS150 with brain somatic mutations in SLC25A2 . These T2-weighted images demonstrate no remarkable findings in the brain parenchyma, including the temporal lobe. Yellow arrowhead: putative regions of epileptic focus. (B) Histopathologic images from H E staining and immunohistochemical (IHC) staining from EPI219 (upper panels) and LGS150 (lower panels) brain tissues. Black arrowheads: scattered neuron in white matter. Scale bars, 40 μm in H E staining and 200 μm in IHC staining for NeuN, a neuronal marker (C) Capture image from integrative genomic viewer (IGV) (upper panels), showing the results of site-specific amplicon sequencing. Schematic tables (lower panels) showing the number of sequence reads counted as mutated or reference sequences, as well as the VAFs of mutated alleles. Mut: mutation, Ref: reference.

    Journal: Neurology: Genetics

    Article Title: Brain somatic mutations in SLC35A2 cause intractable epilepsy with aberrant N-glycosylation

    doi: 10.1212/NXG.0000000000000294

    Figure Lengend Snippet: Representative radiologic and pathologic images of patients with brain somatic mutations in SLC35A2 (A) Preoperative and postoperative brain MRI T2-weighted images from patients EPI219 and LGS150 with brain somatic mutations in SLC25A2 . These T2-weighted images demonstrate no remarkable findings in the brain parenchyma, including the temporal lobe. Yellow arrowhead: putative regions of epileptic focus. (B) Histopathologic images from H E staining and immunohistochemical (IHC) staining from EPI219 (upper panels) and LGS150 (lower panels) brain tissues. Black arrowheads: scattered neuron in white matter. Scale bars, 40 μm in H E staining and 200 μm in IHC staining for NeuN, a neuronal marker (C) Capture image from integrative genomic viewer (IGV) (upper panels), showing the results of site-specific amplicon sequencing. Schematic tables (lower panels) showing the number of sequence reads counted as mutated or reference sequences, as well as the VAFs of mutated alleles. Mut: mutation, Ref: reference.

    Article Snippet: Briefly, this method calculates the discrepancy between expected and observed amounts of mismatches in amplicon-based, Illumina platform data sets (up to 10,000X) in which 2 independent blood samples with known single nucleotide polymorphisms (SNPs) were mixed to mimic somatic mutations with 4 different VAFs: 0.5%, 1%, 5%, and 10%.

    Techniques: Magnetic Resonance Imaging, Staining, Immunohistochemistry, Marker, Amplification, Sequencing, Mutagenesis

    Experimental design. ( a ) Design of single and dual-index sequencing strategy and schematic describing the 3 amplicon designs: Fusion Primer Design (A) is a one step PCR which uses a single 12-nt error-correcting Golay index sequence (blue) allowing a high multiplexing capability. Tag tailed design (B) is a 2-step PCR which uses a universal primer for the first step and a dual index barcoded primer set in the second step. Standard Illumina Nextera 8-nt index sequences were used (pink Index 5; blue Index 7). The Pac Bio Ligate Adapters design (C): Two harpin adapters (grey) were ligated to a barcoded template (BF forward barcode; BR reverse barcode) to allow multiplexing. ( b ) Platform Specific Amplicon Libraries: Illumina paired-end sequencing (1,2) generates 2 sequencing reads (R1 and R2) per each cluster and can have single (Standard/Golay) or dual indexes (I5, I7). Ion Torrent and 454 (3) have a single read for each bead with a single index (MID). Pacific Bioscience generate a single circular read for each molecule (SMRT bell) and can have one (BF or BR) or two indexes. The starting point and direction of sequencing reads are indicated by a solid blue line and arrows, respectively. In the case of Fusion Primer Design custom sequencing primer were used

    Journal: BMC Genomics

    Article Title: A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

    doi: 10.1186/s12864-015-2194-9

    Figure Lengend Snippet: Experimental design. ( a ) Design of single and dual-index sequencing strategy and schematic describing the 3 amplicon designs: Fusion Primer Design (A) is a one step PCR which uses a single 12-nt error-correcting Golay index sequence (blue) allowing a high multiplexing capability. Tag tailed design (B) is a 2-step PCR which uses a universal primer for the first step and a dual index barcoded primer set in the second step. Standard Illumina Nextera 8-nt index sequences were used (pink Index 5; blue Index 7). The Pac Bio Ligate Adapters design (C): Two harpin adapters (grey) were ligated to a barcoded template (BF forward barcode; BR reverse barcode) to allow multiplexing. ( b ) Platform Specific Amplicon Libraries: Illumina paired-end sequencing (1,2) generates 2 sequencing reads (R1 and R2) per each cluster and can have single (Standard/Golay) or dual indexes (I5, I7). Ion Torrent and 454 (3) have a single read for each bead with a single index (MID). Pacific Bioscience generate a single circular read for each molecule (SMRT bell) and can have one (BF or BR) or two indexes. The starting point and direction of sequencing reads are indicated by a solid blue line and arrows, respectively. In the case of Fusion Primer Design custom sequencing primer were used

    Article Snippet: Amplicon libraries were sequenced on 454 GS FLX/FLX+, Illumina MiSeq (MS), Life Technologies Ion Torrent (IT) and Pacific Bioscience RS II (PB) platforms, to determine the impact of different experimental conditions on the community structure.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Multiplexing

    Assessment of conventional algorithms for detecting mutations with low-allele frequency. a Schematic of experimental design for test-base sequencing data. Four distinct sample mixtures (A, B, C, and D) were prepared and sequenced with three different sequencing platforms (ILH, ILA, and ITA). Constructed libraries from each platform were sequenced twice to produce sequencing replicates (X 11 and X 12 ). For samples A and B, two independent sets of sequencing library were additionally prepared to sequence data from library replicates (X 21 and X 31 ). Each set of sequencing data was sequentially downsampled ten times to evaluate the effects of read depth. All generated datasets were analyzed, and average performances were reported for each depth and platform. b Sensitivity and FPR of conventional methods (MuTect with adjusted parameters, others in Supplementary Figs. 1 and 2 ) by sequencing depth and VAF for each sequencing platform. Points are depicted within the maximum depth of the sequencing data (Supplementary Table 1 ). Error bars, 95% confidence intervals. Source data are provided as a Source Data file. c Distribution of allele frequencies and probabilistic odd-ratio scores (LOD T ) for true-positive and false-positive calls for each sample mixture (colored by blue and red, respectively). ILH hybrid-capture-based Illumina sequencing, ILA amplicon-based Illumina sequencing, ITA amplicon-based Ion Torrent sequencing, VAF variant allele frequency, FPR false-positive rate

    Journal: Nature Communications

    Article Title: The use of technical replication for detection of low-level somatic mutations in next-generation sequencing

    doi: 10.1038/s41467-019-09026-y

    Figure Lengend Snippet: Assessment of conventional algorithms for detecting mutations with low-allele frequency. a Schematic of experimental design for test-base sequencing data. Four distinct sample mixtures (A, B, C, and D) were prepared and sequenced with three different sequencing platforms (ILH, ILA, and ITA). Constructed libraries from each platform were sequenced twice to produce sequencing replicates (X 11 and X 12 ). For samples A and B, two independent sets of sequencing library were additionally prepared to sequence data from library replicates (X 21 and X 31 ). Each set of sequencing data was sequentially downsampled ten times to evaluate the effects of read depth. All generated datasets were analyzed, and average performances were reported for each depth and platform. b Sensitivity and FPR of conventional methods (MuTect with adjusted parameters, others in Supplementary Figs. 1 and 2 ) by sequencing depth and VAF for each sequencing platform. Points are depicted within the maximum depth of the sequencing data (Supplementary Table 1 ). Error bars, 95% confidence intervals. Source data are provided as a Source Data file. c Distribution of allele frequencies and probabilistic odd-ratio scores (LOD T ) for true-positive and false-positive calls for each sample mixture (colored by blue and red, respectively). ILH hybrid-capture-based Illumina sequencing, ILA amplicon-based Illumina sequencing, ITA amplicon-based Ion Torrent sequencing, VAF variant allele frequency, FPR false-positive rate

    Article Snippet: The test-base data set consisted of library- and sequencing-level replicates for three distinct platforms: hybridization-capture-based Illumina sequencing (ILH, up to 1000×) and amplicon-based Illumina and Ion Torrent sequencing (ILA and ITA, respectively, up to 10,000×) (see Methods).

    Techniques: Sequencing, Construct, Generated, Amplification, Variant Assay

    Representative image of an agarose gel electrophoresis for the amplicons COI-lf and 16S-sf ( 1 = A. brevispinosa 37,334 A2, 2 = A. brevispinosa 37,334 A1, 3 = A. arbustorum 86,813 A2, 4 = A. arbustorum 100,810 A1, 5 = D. polymorpha 101,850, 6 = D. polymorpha 83,846 B1, 7 = H. pomatia 74,402 B2, 8 = P. planorbis 84,060 A2, C = Negative control)

    Journal: BMC Research Notes

    Article Title: DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods

    doi: 10.1186/s13104-016-2147-7

    Figure Lengend Snippet: Representative image of an agarose gel electrophoresis for the amplicons COI-lf and 16S-sf ( 1 = A. brevispinosa 37,334 A2, 2 = A. brevispinosa 37,334 A1, 3 = A. arbustorum 86,813 A2, 4 = A. arbustorum 100,810 A1, 5 = D. polymorpha 101,850, 6 = D. polymorpha 83,846 B1, 7 = H. pomatia 74,402 B2, 8 = P. planorbis 84,060 A2, C = Negative control)

    Article Snippet: To test whether the amplified amplicons are the expected gene sequences, a subset of samples was sequenced (LGC Genomics, Berlin) using the same primers used for producing the amplicons.

    Techniques: Agarose Gel Electrophoresis, Negative Control

    Human defensin gene clusters at 8p23.1 (NCBI build 36, hg18) and location of the amplicons analyzed by 454 (F1-8) and cloning/Sanger (S1-2) sequencing within the proximal DEFB (DEF cluster b2) .

    Journal: BMC Genomics

    Article Title: Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

    doi: 10.1186/1471-2164-11-252

    Figure Lengend Snippet: Human defensin gene clusters at 8p23.1 (NCBI build 36, hg18) and location of the amplicons analyzed by 454 (F1-8) and cloning/Sanger (S1-2) sequencing within the proximal DEFB (DEF cluster b2) .

    Article Snippet: The pools were diluted and subjected to emulsion PCR following the FLX emPCR protocol for amplicons (Roche Diagnostics, December 2007) using both emPCR kits II (primer A) and III (primer B) and sequenced on a GS FLX (Roche Diagnostics) by both primers on 1 lane/pool of a 16-lane gasket on a 70 × 75 FLX picotiterplate.

    Techniques: Clone Assay, Sequencing

    rb1 mutant alleles and allele frequencies in somatic, germline, and tumor tissues from adult genetic mosaic zebrafish. ( a ) 14 different indel alleles in rb1 exon 2 were identified in retina, muscle, and germline genomic DNA from two adults. Mutant alleles represented 33% of cloned amplicons. In tumor tissue 8 unique alleles were identified, representing 87% of cloned amplicons. ( b ) Two frameshift alleles that delete 11 bp and 19 bp in rb1 exon 3 were detected in two adults. 10% of sequenced clones were mutant in retina, muscle or germline tissue. In tumor tissue 68% of sequenced clones were mutant alleles. Red arrows mark TALEN cut site.

    Journal: Scientific Reports

    Article Title: Rapid tumor induction in zebrafish by TALEN-mediated somatic inactivation of the retinoblastoma1 tumor suppressor rb1

    doi: 10.1038/srep13745

    Figure Lengend Snippet: rb1 mutant alleles and allele frequencies in somatic, germline, and tumor tissues from adult genetic mosaic zebrafish. ( a ) 14 different indel alleles in rb1 exon 2 were identified in retina, muscle, and germline genomic DNA from two adults. Mutant alleles represented 33% of cloned amplicons. In tumor tissue 8 unique alleles were identified, representing 87% of cloned amplicons. ( b ) Two frameshift alleles that delete 11 bp and 19 bp in rb1 exon 3 were detected in two adults. 10% of sequenced clones were mutant in retina, muscle or germline tissue. In tumor tissue 68% of sequenced clones were mutant alleles. Red arrows mark TALEN cut site.

    Article Snippet: Amplicons were TOPO cloned (Invitrogen), and 50–100 individual clones sequenced per sample.

    Techniques: Mutagenesis, Clone Assay

    GLI binds the 5′ end of Tsix A. Coomassie blue stained gel of recombinant proteins used in EMSA. B, C, D. DNA EMSA with the indicated proteins and probes. GLI motifs (green) and mutated positions (red) in the probes are shown. 2pmoles of DNA probes; 2pmoles of GFP; and 0.5, 1, 2pmoles of GLI1-zfd were used in B and C. 2pmoles of GFP or GLI1-zfd; 2pmoles DXPas34 probe; and 5, 10, and 20pmoles of DXPas34 wildtype or mutated cold competitor probes were used in D. E. ChIP-PCR from GLI2-3×FLAG ES cells grown for 72hrs with 100nM SAG and 1µg/mL doxycycline. GLI2-FLAG IP, normal IgG IP, and Input PCR products for each amplicon are shown. F. GLI1-3×FLAG and GLI2-3×FLAG ChIP-seq for positive control, Ptch1. Peaks were called from intersected datasets from two biological replicates following input normalization. G. CEAS analysis of GLI1-3×FLAG (middle) and GLI2-3×FLAG (right) ChIP-seq from undifferentiated female ES cells treated with SAG. Genomic elements are defined in the accompanying key (left). Genomic distribution of each element indicated as a %. H. ChIP-seq analysis of GLI1 (scale, 0–3) in d0 and d3 male and female ES cells, with d0 female CTCF track for comparison. Tracks are displayed in IGV for the Xite-Tsix-Xist region. I. Probability plot for the likelihood of finding a CTCF site at indicated distances (in kb) from a GLI site. Solid line, observed. Dotted line, randomized model wherein CTCF sites are randomly shuffled throughout the genome.

    Journal: Developmental cell

    Article Title: Genetic intersection of Tsix and Hedgehog signaling during the initiation of X-chromosome inactivation

    doi: 10.1016/j.devcel.2017.09.027

    Figure Lengend Snippet: GLI binds the 5′ end of Tsix A. Coomassie blue stained gel of recombinant proteins used in EMSA. B, C, D. DNA EMSA with the indicated proteins and probes. GLI motifs (green) and mutated positions (red) in the probes are shown. 2pmoles of DNA probes; 2pmoles of GFP; and 0.5, 1, 2pmoles of GLI1-zfd were used in B and C. 2pmoles of GFP or GLI1-zfd; 2pmoles DXPas34 probe; and 5, 10, and 20pmoles of DXPas34 wildtype or mutated cold competitor probes were used in D. E. ChIP-PCR from GLI2-3×FLAG ES cells grown for 72hrs with 100nM SAG and 1µg/mL doxycycline. GLI2-FLAG IP, normal IgG IP, and Input PCR products for each amplicon are shown. F. GLI1-3×FLAG and GLI2-3×FLAG ChIP-seq for positive control, Ptch1. Peaks were called from intersected datasets from two biological replicates following input normalization. G. CEAS analysis of GLI1-3×FLAG (middle) and GLI2-3×FLAG (right) ChIP-seq from undifferentiated female ES cells treated with SAG. Genomic elements are defined in the accompanying key (left). Genomic distribution of each element indicated as a %. H. ChIP-seq analysis of GLI1 (scale, 0–3) in d0 and d3 male and female ES cells, with d0 female CTCF track for comparison. Tracks are displayed in IGV for the Xite-Tsix-Xist region. I. Probability plot for the likelihood of finding a CTCF site at indicated distances (in kb) from a GLI site. Solid line, observed. Dotted line, randomized model wherein CTCF sites are randomly shuffled throughout the genome.

    Article Snippet: Primer efficiencies were calculated using titrated DNA for each target amplicon (Nanodrop, ThermoFisher).

    Techniques: Staining, Recombinant, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Amplification, Positive Control

    Distribution of newly identified gene mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Journal: Blood Cancer Journal

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas

    doi: 10.1038/bcj.2016.122

    Figure Lengend Snippet: Distribution of newly identified gene mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Article Snippet: Amplicon-based sequencing The libraries were prepared using the Ion Plus Fragment Library Kit according to the protocol for preparing short amplicon libraries (Life Technologies).

    Techniques: Sequencing, Amplification

    B-cell-specific mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively. NOTCH1 is marked by red letters because this is repetitive.

    Journal: Blood Cancer Journal

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas

    doi: 10.1038/bcj.2016.122

    Figure Lengend Snippet: B-cell-specific mutations in nodal T-cell lymphomas. The results of Sanger sequencing and/or amplicon-based deep sequencing for some newly identified gene mutations in whole tumor, PD1+ cells and CD20+ cells are shown. The numeric values indicate allele frequencies of mutations defined by deep sequencing. The AITL samples are indicated in black letters. The PTCL-NOS/nodal PTCL with TFH phenotype sample is indicated in blue letters. NA, not analyzed by deep sequencing. The filled and dashed red arrows indicate mutations and no mutations, respectively. NOTCH1 is marked by red letters because this is repetitive.

    Article Snippet: Amplicon-based sequencing The libraries were prepared using the Ion Plus Fragment Library Kit according to the protocol for preparing short amplicon libraries (Life Technologies).

    Techniques: Sequencing, Amplification

    RHOA mutations are specific to PD1+ cells. ( a ) An example of the immunostaining pattern for PD1 and CD20 in AITL. Left, PD1+ cells; right, CD20+ cells. ( b ) Sequences of G17V RHOA mutations in whole tumor, PD1+ cells and CD20+ cells. The numeric values indicate allele frequencies of mutations defined by amplicon-based deep sequencing. The AITL samples are indicated in black letters. The nodal PTCL with TFH phenotype sample is indicated in red letters *: RHOA c.A51T:p.G17V, silent mutation. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Journal: Blood Cancer Journal

    Article Title: Identification of cell-type-specific mutations in nodal T-cell lymphomas

    doi: 10.1038/bcj.2016.122

    Figure Lengend Snippet: RHOA mutations are specific to PD1+ cells. ( a ) An example of the immunostaining pattern for PD1 and CD20 in AITL. Left, PD1+ cells; right, CD20+ cells. ( b ) Sequences of G17V RHOA mutations in whole tumor, PD1+ cells and CD20+ cells. The numeric values indicate allele frequencies of mutations defined by amplicon-based deep sequencing. The AITL samples are indicated in black letters. The nodal PTCL with TFH phenotype sample is indicated in red letters *: RHOA c.A51T:p.G17V, silent mutation. The filled and dashed red arrows indicate mutations and no mutations, respectively.

    Article Snippet: Amplicon-based sequencing The libraries were prepared using the Ion Plus Fragment Library Kit according to the protocol for preparing short amplicon libraries (Life Technologies).

    Techniques: Immunostaining, Amplification, Sequencing, Mutagenesis

    Induction of HCV escape from a direct acting antiviral in HFBR. ( a ) Timeline of Huh7.5 cell cultivation in DMEM + 10%FBS and serum-free AEM, indicating infection with HCV and initiation of treatment with different concentrations of the NS5A inhibitor daclatasvir (DCV). HCV from HFBR harvests (1000 μL, 50 μL or 5 μL) were used for infection of 10 6 Huh7.5 cells plated the previous day in T25 cell culture flasks (derived cultures). Peak infectivity titers in derived cultures are reported. Amino acid at NS5A position 93 according to the H77 reference sequence (GenBank accession no AF009606) was determined by Sanger sequencing for selected harvests and derived cultures. *, H at position 93 was present in ~50% of viral genomes. ( b ) 8 × 10 7 Huh7.5 cells were seeded in a hollow fiber bioreactor in DMEM + 10% FBS and infected with 1.25 × 10 6 FFU of HCV third passage stock on day 5 post cell seeding, when glucose consumption was 590 mg/day (arrow). At day 9 post cell seeding DMEM was replaced with serum-free AEM. Treatment with daclatasvir at 7.8 nM (corresponding to 64 x EC50 29 ) was initiated at day 27 post cell seeding; at day 45 the concentration was increased to 124.2 nM (corresponding to 1024 x EC50). On day 59 the treatment was terminated. ( c and d ) Determination of HCV infectivity titers and HCV RNA titers were carried out as described in Fig. 2 . *, indicates HCV infectivity titers below assay detection level. ( e ) HCV from harvest 9, 12 and 16 were loaded on 10–40% iodixanol gradients. Following ultracentrifugation 18 fractions were collected as in Fig. 5 . HCV infectivity and HCV RNA titers of each fraction were determined as described for Fig. 2 . ( f ) RNA extracted from harvest 9, 12 and 14 at 1-, 10-, 100- and 1000-fold dilution was used for RT-PCR for generation of a full-length amplicon spanning the complete HCV ORF. PCR products were visualized on a 1% agarose gel including a 1 kb DNA ladder; expected positions of full-length amplicons are indicated by arrows. Gel image was cropped as indicated by boxes; full-length gel is presented in Supplementary Fig. S4 .

    Journal: Scientific Reports

    Article Title: High density Huh7.5 cell hollow fiber bioreactor culture for high-yield production of hepatitis C virus and studies of antivirals

    doi: 10.1038/s41598-018-35010-5

    Figure Lengend Snippet: Induction of HCV escape from a direct acting antiviral in HFBR. ( a ) Timeline of Huh7.5 cell cultivation in DMEM + 10%FBS and serum-free AEM, indicating infection with HCV and initiation of treatment with different concentrations of the NS5A inhibitor daclatasvir (DCV). HCV from HFBR harvests (1000 μL, 50 μL or 5 μL) were used for infection of 10 6 Huh7.5 cells plated the previous day in T25 cell culture flasks (derived cultures). Peak infectivity titers in derived cultures are reported. Amino acid at NS5A position 93 according to the H77 reference sequence (GenBank accession no AF009606) was determined by Sanger sequencing for selected harvests and derived cultures. *, H at position 93 was present in ~50% of viral genomes. ( b ) 8 × 10 7 Huh7.5 cells were seeded in a hollow fiber bioreactor in DMEM + 10% FBS and infected with 1.25 × 10 6 FFU of HCV third passage stock on day 5 post cell seeding, when glucose consumption was 590 mg/day (arrow). At day 9 post cell seeding DMEM was replaced with serum-free AEM. Treatment with daclatasvir at 7.8 nM (corresponding to 64 x EC50 29 ) was initiated at day 27 post cell seeding; at day 45 the concentration was increased to 124.2 nM (corresponding to 1024 x EC50). On day 59 the treatment was terminated. ( c and d ) Determination of HCV infectivity titers and HCV RNA titers were carried out as described in Fig. 2 . *, indicates HCV infectivity titers below assay detection level. ( e ) HCV from harvest 9, 12 and 16 were loaded on 10–40% iodixanol gradients. Following ultracentrifugation 18 fractions were collected as in Fig. 5 . HCV infectivity and HCV RNA titers of each fraction were determined as described for Fig. 2 . ( f ) RNA extracted from harvest 9, 12 and 14 at 1-, 10-, 100- and 1000-fold dilution was used for RT-PCR for generation of a full-length amplicon spanning the complete HCV ORF. PCR products were visualized on a 1% agarose gel including a 1 kb DNA ladder; expected positions of full-length amplicons are indicated by arrows. Gel image was cropped as indicated by boxes; full-length gel is presented in Supplementary Fig. S4 .

    Article Snippet: Obtained amplicons were subjected to Sanger sequencing (Macrogen Europe).

    Techniques: Infection, Cell Culture, Derivative Assay, Sequencing, Concentration Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis

    Analytic detection limits of chemically and enzymatically labeled amplicons. The amplicons were serially diluted and hybridized for 1.5 h at 53°C. The error bars represent the standard deviation. The samples were run in duplicate, and the experiments

    Journal: Limnology and oceanography, methods / ASLO

    Article Title: Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology

    doi: 10.4319/lom.2010.8.269

    Figure Lengend Snippet: Analytic detection limits of chemically and enzymatically labeled amplicons. The amplicons were serially diluted and hybridized for 1.5 h at 53°C. The error bars represent the standard deviation. The samples were run in duplicate, and the experiments

    Article Snippet: Chemically labeled amplicons (Mirus Label IT amplicons): For chemically labeled amplicons, illustrates the detection levels of the assay conducted at 53°C.

    Techniques: Labeling, Standard Deviation

    Performance of species-specific probes with field samples. Hybridization assay conditions used 15 μL chemical-labeled IT amplicon. The amplicons were generated using 40 cycles, and amplification was done with the universal primer set D2C and DIRF.

    Journal: Limnology and oceanography, methods / ASLO

    Article Title: Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology

    doi: 10.4319/lom.2010.8.269

    Figure Lengend Snippet: Performance of species-specific probes with field samples. Hybridization assay conditions used 15 μL chemical-labeled IT amplicon. The amplicons were generated using 40 cycles, and amplification was done with the universal primer set D2C and DIRF.

    Article Snippet: Chemically labeled amplicons (Mirus Label IT amplicons): For chemically labeled amplicons, illustrates the detection levels of the assay conducted at 53°C.

    Techniques: Hybridization, Labeling, Amplification, Generated

    Comparison of Mirus Label IT and 5′ end labeled amplicons. Fifty nanograms of the labeled template was hybridized with different sets of K. brevis (Pkb, Pkb2, PKB658, Pkb2lna, PKB658lna) and K. mikimotoi probes (Pkmiklna and Pkmiklna2). Hybridization

    Journal: Limnology and oceanography, methods / ASLO

    Article Title: Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology

    doi: 10.4319/lom.2010.8.269

    Figure Lengend Snippet: Comparison of Mirus Label IT and 5′ end labeled amplicons. Fifty nanograms of the labeled template was hybridized with different sets of K. brevis (Pkb, Pkb2, PKB658, Pkb2lna, PKB658lna) and K. mikimotoi probes (Pkmiklna and Pkmiklna2). Hybridization

    Article Snippet: Chemically labeled amplicons (Mirus Label IT amplicons): For chemically labeled amplicons, illustrates the detection levels of the assay conducted at 53°C.

    Techniques: Labeling, Hybridization

    Specificity of probes with Mirus Label IT D1/D2 amplicons. Probes were challenged with closely and non–closely related algal species. The hybridization was carried out for 1.5 h at 53°C and used 33 ng amplicon per well. The samples were

    Journal: Limnology and oceanography, methods / ASLO

    Article Title: Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology

    doi: 10.4319/lom.2010.8.269

    Figure Lengend Snippet: Specificity of probes with Mirus Label IT D1/D2 amplicons. Probes were challenged with closely and non–closely related algal species. The hybridization was carried out for 1.5 h at 53°C and used 33 ng amplicon per well. The samples were

    Article Snippet: Chemically labeled amplicons (Mirus Label IT amplicons): For chemically labeled amplicons, illustrates the detection levels of the assay conducted at 53°C.

    Techniques: Hybridization, Amplification

    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv amplicons. S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.

    Journal: Frontiers in Immunology

    Article Title: Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library

    doi: 10.3389/fimmu.2017.01796

    Figure Lengend Snippet: Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv amplicons. S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.

    Article Snippet: Amplicons were cleaned using 1× ratio of AMPure PB Beads (Pacific Biosciences).

    Techniques: Plasmid Preparation, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis

    Canary read alignment. Overlapping amplicon reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants

    Journal: BMC Bioinformatics

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

    doi: 10.1186/s12859-017-1950-z

    Figure Lengend Snippet: Canary read alignment. Overlapping amplicon reads are aligned to the reference genome in a two step process. The overlapping read pairs, that are derived from the same DNA molecule, are aligned to each other to form a single consensus merged read which is then aligned to a reference genome to identify variants

    Article Snippet: There are relatively few options for processing amplicon data outside of commercial platforms such as Illumina BaseSpace [ ].

    Techniques: Amplification, Derivative Assay

    Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by amplicon sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.

    Journal: Microbes and Environments

    Article Title: Ureolytic Prokaryotes in Soil: Community Abundance and Diversity

    doi: 10.1264/jsme2.ME17188

    Figure Lengend Snippet: Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by amplicon sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.

    Article Snippet: On the other hand, the community structure of ureolytic prokaryotes was investigated in the present study using amplicon sequencing without biological replicates; therefore, further verification studies are required in order to clarify how widespread site-specific OTUs are.

    Techniques: Amplification, Sequencing, Construct