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  • 99
    Vector Laboratories ngs
    Ngs, supplied by Vector Laboratories, used in various techniques. Bioz Stars score: 99/100, based on 660 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore ng dimethylarginine
    Detection of symmetric <t>dimethylarginine</t> (SDMA) as a minor product in histone H2A incubated with Hsl7 for extended times. Amino acid analysis of histone H2A methylation in wild type GST-Hsl7 (panel A) and mutant GST-Hsl7 G387A (panel B) incubations for
    Ng Dimethylarginine, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    fluidigm ngs ngs
    Detection of symmetric <t>dimethylarginine</t> (SDMA) as a minor product in histone H2A incubated with Hsl7 for extended times. Amino acid analysis of histone H2A methylation in wild type GST-Hsl7 (panel A) and mutant GST-Hsl7 G387A (panel B) incubations for
    Ngs Ngs, supplied by fluidigm, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    The Jackson Laboratory rosa26 nt ng nt ng
    Detection of symmetric <t>dimethylarginine</t> (SDMA) as a minor product in histone H2A incubated with Hsl7 for extended times. Amino acid analysis of histone H2A methylation in wild type GST-Hsl7 (panel A) and mutant GST-Hsl7 G387A (panel B) incubations for
    Rosa26 Nt Ng Nt Ng, supplied by The Jackson Laboratory, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc ngs
    ( A ) A schematic diagram shows the experimental procedures. The 22-mer lesion-containing ODNs with barcodes were ligated to the EcoR I-linearized M13 vector, mixed at equal amounts and subjected to in vivo replication. The harvested M13 progenies were amplified with barcoded <t>PCR</t> primers, and equal amounts of PCR products from different cell lines were mixed and ligated with PE adapters. The ligation products were further amplified using PE PCR primers, and the resulting PCR products were purified and subjected to <t>NGS</t> analysis. ( B ) Detailed sequence information for the PCR amplification of progeny genome, adapter ligation, and PCR amplification for the construction of sequencing library. ‘X’, ‘P’ and ‘Q’ represent the lesion, the DNA base after in vivo replication of DNA lesion, and the paired nucleobase of ‘P’ in the complementary strand, respectively. ‘BB’ in green and blue represent lesion-specific barcode and the barcode for host cell lines and biological replicates, respectively.
    Ngs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 2041 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Diagenode bioruptor ngs
    ( A ) A schematic diagram shows the experimental procedures. The 22-mer lesion-containing ODNs with barcodes were ligated to the EcoR I-linearized M13 vector, mixed at equal amounts and subjected to in vivo replication. The harvested M13 progenies were amplified with barcoded <t>PCR</t> primers, and equal amounts of PCR products from different cell lines were mixed and ligated with PE adapters. The ligation products were further amplified using PE PCR primers, and the resulting PCR products were purified and subjected to <t>NGS</t> analysis. ( B ) Detailed sequence information for the PCR amplification of progeny genome, adapter ligation, and PCR amplification for the construction of sequencing library. ‘X’, ‘P’ and ‘Q’ represent the lesion, the DNA base after in vivo replication of DNA lesion, and the paired nucleobase of ‘P’ in the complementary strand, respectively. ‘BB’ in green and blue represent lesion-specific barcode and the barcode for host cell lines and biological replicates, respectively.
    Bioruptor Ngs, supplied by Diagenode, used in various techniques. Bioz Stars score: 91/100, based on 425 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Santa Cruz Biotechnology ngs pbst
    ( A ) A schematic diagram shows the experimental procedures. The 22-mer lesion-containing ODNs with barcodes were ligated to the EcoR I-linearized M13 vector, mixed at equal amounts and subjected to in vivo replication. The harvested M13 progenies were amplified with barcoded <t>PCR</t> primers, and equal amounts of PCR products from different cell lines were mixed and ligated with PE adapters. The ligation products were further amplified using PE PCR primers, and the resulting PCR products were purified and subjected to <t>NGS</t> analysis. ( B ) Detailed sequence information for the PCR amplification of progeny genome, adapter ligation, and PCR amplification for the construction of sequencing library. ‘X’, ‘P’ and ‘Q’ represent the lesion, the DNA base after in vivo replication of DNA lesion, and the paired nucleobase of ‘P’ in the complementary strand, respectively. ‘BB’ in green and blue represent lesion-specific barcode and the barcode for host cell lines and biological replicates, respectively.
    Ngs Pbst, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Pacific Biosciences ngs platforms
    Comparison of data processing across <t>NGS</t> platforms. Number of sequencing errors, substitutions, deletions, and insertions (per read) for the NGS platforms: 454™, Illumina®, <t>PacBio®,</t> and Ion Torrent™. The mean and interquartile range (IQR) are indicated for each sample. Whiskers indicate 1.5 times the IQR as is the default value in the R-statistical package [75] .
    Ngs Platforms, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 168 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Roche ngs sequencer
    Comparison of data processing across <t>NGS</t> platforms. Number of sequencing errors, substitutions, deletions, and insertions (per read) for the NGS platforms: 454™, Illumina®, <t>PacBio®,</t> and Ion Torrent™. The mean and interquartile range (IQR) are indicated for each sample. Whiskers indicate 1.5 times the IQR as is the default value in the R-statistical package [75] .
    Ngs Sequencer, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Roche ngs technologies
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    Ngs Technologies, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 526 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Anatrace β ng
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    β Ng, supplied by Anatrace, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc miseq ngs
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    Miseq Ngs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Accelrys ngs analysis
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    Ngs Analysis, supplied by Accelrys, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Oxford Nanopore ngs platform
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    Ngs Platform, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 93/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Pacific Biosciences ngs scaffolds
    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each <t>NGS</t> platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the <t>PacBio</t> data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.
    Ngs Scaffolds, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Detection of symmetric dimethylarginine (SDMA) as a minor product in histone H2A incubated with Hsl7 for extended times. Amino acid analysis of histone H2A methylation in wild type GST-Hsl7 (panel A) and mutant GST-Hsl7 G387A (panel B) incubations for

    Journal:

    Article Title: Hsl7 is a substrate-specific type II protein arginine methyltransferase in yeast

    doi: 10.1016/j.bbrc.2008.05.121

    Figure Lengend Snippet: Detection of symmetric dimethylarginine (SDMA) as a minor product in histone H2A incubated with Hsl7 for extended times. Amino acid analysis of histone H2A methylation in wild type GST-Hsl7 (panel A) and mutant GST-Hsl7 G387A (panel B) incubations for

    Article Snippet: The hydrolyzed sample was added to 50 μl of water and 500 μl of citrate buffer (0.2 M Na+ , pH 2.2) along with 1.0 μmol each of unlabeled standards of ω- N G – monomethylarginine (acetate salt, Sigma Chemical, St. Louis, MO)( ω-MMA) and ω- NG , NG -dimethylarginine (hydrochloride, Sigma Chemical, St. Louis, MO)(ADMA), and ω- NG , NG -dimethylarginine (di(p-hydroxyazobenzene-p’-sulfonate) salt, Sigma Chemical, St. Louis, MO)(SDMA).

    Techniques: Incubation, Methylation, Mutagenesis

    PRMT9 catalyzes symmetrical dimethylation of SAP145 at Arginine 508 ( a ) PRMT9 methylates SAP145 fragment F3 (a.a. 401–550). The in vitro methylation was performed by incubating either wild type or enzymatic mutant recombinant HA-PRMT9 (purified from Sf21 cells) with GST or GST-tag SAP145 fragments (F1–F4, as described in Fig. 3a and b ). The loading of PRMT9 was detected by western blotting using αHA antibody. ( b ) PRMT9 symmetrically dimethylates SAP145 as detected by amino acid analysis. Amino acid analysis of in vitro methylation products from wild type and enzymatic mutant GFP-PRMT9 as enzymes and GST-SAP145 (401–550) fragment as substrate. Black dashed line indicates elution of nonradiolabeled standards. The radioactive peaks elute 1–2 min before the nonradiolabeled standards due to a tritium isotope effect 39 . ( c ) PRMT9 symmetrically dimethylates SAP145 as detected by thin layer chromatography (TLC). SDMA fractions from cation-exchange chromatography of the in vitro 3 H-methylation reaction were separated using thin layer chromatography (TLC). Fractions were spotted on a cellulose plate along with the addition of 5 nmol MMA, 15 nmol ADMA, and 5 nmol SDMA internal standards. Individual standards were also spotted in adjacent lanes to determine the migration distance of each methylated arginine derivative. The origin is indicated by fraction 2. The solvent front was run near the end of the plate to fraction 32. The plate was air-dried and each lane was subsequently sliced in 5 mm fractions and counted for three 30-min counting cycles. The radioactive peaks elute 1–2 min before the nonradiolabeled standards due to a tritium isotope effect 39 . This experiment was repeated 3 times and similar migration patterns were observed. ( d ) PRMT9 methylates SAP145 at R508 in vitro . The in vitro methylation assay was performed by incubating recombinant HA-PRMT9 with a series of Arg to Lys (R to K) mutants of SAP145 fragment F3 (see Fig. 3a and b for description) for 1 h at 30° C. After exposure at −80 °C for 3 days, the membrane was stained with Coomassie blue to check the protein loading. Arrows indicate the positions of the substrates and stars indicate the positions of the recombinant HA-PRMT9.

    Journal: Nature communications

    Article Title: PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145

    doi: 10.1038/ncomms7428

    Figure Lengend Snippet: PRMT9 catalyzes symmetrical dimethylation of SAP145 at Arginine 508 ( a ) PRMT9 methylates SAP145 fragment F3 (a.a. 401–550). The in vitro methylation was performed by incubating either wild type or enzymatic mutant recombinant HA-PRMT9 (purified from Sf21 cells) with GST or GST-tag SAP145 fragments (F1–F4, as described in Fig. 3a and b ). The loading of PRMT9 was detected by western blotting using αHA antibody. ( b ) PRMT9 symmetrically dimethylates SAP145 as detected by amino acid analysis. Amino acid analysis of in vitro methylation products from wild type and enzymatic mutant GFP-PRMT9 as enzymes and GST-SAP145 (401–550) fragment as substrate. Black dashed line indicates elution of nonradiolabeled standards. The radioactive peaks elute 1–2 min before the nonradiolabeled standards due to a tritium isotope effect 39 . ( c ) PRMT9 symmetrically dimethylates SAP145 as detected by thin layer chromatography (TLC). SDMA fractions from cation-exchange chromatography of the in vitro 3 H-methylation reaction were separated using thin layer chromatography (TLC). Fractions were spotted on a cellulose plate along with the addition of 5 nmol MMA, 15 nmol ADMA, and 5 nmol SDMA internal standards. Individual standards were also spotted in adjacent lanes to determine the migration distance of each methylated arginine derivative. The origin is indicated by fraction 2. The solvent front was run near the end of the plate to fraction 32. The plate was air-dried and each lane was subsequently sliced in 5 mm fractions and counted for three 30-min counting cycles. The radioactive peaks elute 1–2 min before the nonradiolabeled standards due to a tritium isotope effect 39 . This experiment was repeated 3 times and similar migration patterns were observed. ( d ) PRMT9 methylates SAP145 at R508 in vitro . The in vitro methylation assay was performed by incubating recombinant HA-PRMT9 with a series of Arg to Lys (R to K) mutants of SAP145 fragment F3 (see Fig. 3a and b for description) for 1 h at 30° C. After exposure at −80 °C for 3 days, the membrane was stained with Coomassie blue to check the protein loading. Arrows indicate the positions of the substrates and stars indicate the positions of the recombinant HA-PRMT9.

    Article Snippet: To prepare samples for high resolution cation-exchange chromatography, the hydrolyzed samples were resuspended in 50 μl of water and mixed with sodium citrate buffer (0.2 M in Na+, pH 2.2) and standards including 1 μmol each of ω-MMA (acetate salt, Sigma, M7033), SDMA (di(p-hydroxyazobenzene)-p′-sulfonate salt, Sigma, D0390) and ADMA (hydrochloride salt, Sigma, D4268).

    Techniques: In Vitro, Methylation, Mutagenesis, Recombinant, Purification, Western Blot, Thin Layer Chromatography, Chromatography, Migration, Staining

    ( A ) A schematic diagram shows the experimental procedures. The 22-mer lesion-containing ODNs with barcodes were ligated to the EcoR I-linearized M13 vector, mixed at equal amounts and subjected to in vivo replication. The harvested M13 progenies were amplified with barcoded PCR primers, and equal amounts of PCR products from different cell lines were mixed and ligated with PE adapters. The ligation products were further amplified using PE PCR primers, and the resulting PCR products were purified and subjected to NGS analysis. ( B ) Detailed sequence information for the PCR amplification of progeny genome, adapter ligation, and PCR amplification for the construction of sequencing library. ‘X’, ‘P’ and ‘Q’ represent the lesion, the DNA base after in vivo replication of DNA lesion, and the paired nucleobase of ‘P’ in the complementary strand, respectively. ‘BB’ in green and blue represent lesion-specific barcode and the barcode for host cell lines and biological replicates, respectively.

    Journal: Nucleic Acids Research

    Article Title: High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing

    doi: 10.1093/nar/gkr159

    Figure Lengend Snippet: ( A ) A schematic diagram shows the experimental procedures. The 22-mer lesion-containing ODNs with barcodes were ligated to the EcoR I-linearized M13 vector, mixed at equal amounts and subjected to in vivo replication. The harvested M13 progenies were amplified with barcoded PCR primers, and equal amounts of PCR products from different cell lines were mixed and ligated with PE adapters. The ligation products were further amplified using PE PCR primers, and the resulting PCR products were purified and subjected to NGS analysis. ( B ) Detailed sequence information for the PCR amplification of progeny genome, adapter ligation, and PCR amplification for the construction of sequencing library. ‘X’, ‘P’ and ‘Q’ represent the lesion, the DNA base after in vivo replication of DNA lesion, and the paired nucleobase of ‘P’ in the complementary strand, respectively. ‘BB’ in green and blue represent lesion-specific barcode and the barcode for host cell lines and biological replicates, respectively.

    Article Snippet: The ligation products were further amplified using PE PCR primers ( Supplementary Table S1 ), and the resulting PCR products (166bp) were gel-purified and subjected to NGS analysis using Illumina Genome Analyzer IIe system.

    Techniques: Plasmid Preparation, In Vivo, Amplification, Polymerase Chain Reaction, Ligation, Purification, Next-Generation Sequencing, Sequencing

    Simplified workflow for HPV typing using NGS methods. During PCR each sample is uniquely barcoded via the primer pair. The use of multiple barcodes allows for larger number of samples to be tested. NGS has its own chemistry that recognizes the presence of an Illumina Index (Ill Id) for sequencing purposes. During sequencing in the flow cell, as each nucleotide is incorporated releasing a flash of light, a picture is retained and analyzed by specialized software to identify the specific nucleotide incorporated. Raw data files comprise million of sequence reads from a pool of samples that need to be analyzed using bioinformatic tools (3p: 3bp-pad; Ubc: unique forward barcode sequence; 2p: 2bp-pad; FwP: forward primer sequence; HPV target: HPV amplicon of interest; RvP: reverse primer sequence; Gbc: general reverse barcode sequence).

    Journal: Expert review of molecular diagnostics

    Article Title: Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention

    doi: 10.1080/14737159.2017.1293525

    Figure Lengend Snippet: Simplified workflow for HPV typing using NGS methods. During PCR each sample is uniquely barcoded via the primer pair. The use of multiple barcodes allows for larger number of samples to be tested. NGS has its own chemistry that recognizes the presence of an Illumina Index (Ill Id) for sequencing purposes. During sequencing in the flow cell, as each nucleotide is incorporated releasing a flash of light, a picture is retained and analyzed by specialized software to identify the specific nucleotide incorporated. Raw data files comprise million of sequence reads from a pool of samples that need to be analyzed using bioinformatic tools (3p: 3bp-pad; Ubc: unique forward barcode sequence; 2p: 2bp-pad; FwP: forward primer sequence; HPV target: HPV amplicon of interest; RvP: reverse primer sequence; Gbc: general reverse barcode sequence).

    Article Snippet: This includes use of different primer pairs, different NGS platforms (e.g., Illumina) and different bioinformatic pipelines.

    Techniques: Next-Generation Sequencing, Polymerase Chain Reaction, Sequencing, Flow Cytometry, Software, Amplification

    Comparison of data processing across NGS platforms. Number of sequencing errors, substitutions, deletions, and insertions (per read) for the NGS platforms: 454™, Illumina®, PacBio®, and Ion Torrent™. The mean and interquartile range (IQR) are indicated for each sample. Whiskers indicate 1.5 times the IQR as is the default value in the R-statistical package [75] .

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of data processing across NGS platforms. Number of sequencing errors, substitutions, deletions, and insertions (per read) for the NGS platforms: 454™, Illumina®, PacBio®, and Ion Torrent™. The mean and interquartile range (IQR) are indicated for each sample. Whiskers indicate 1.5 times the IQR as is the default value in the R-statistical package [75] .

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing, Sequencing

    Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–172, 10–176, and 10–180 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–172, 10–176, and 10–180 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing, Sequencing

    Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–105, 10–133, and 10–137 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–105, 10–133, and 10–137 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing, Sequencing

    Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–65, 10–69, and 10–73 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence from the respective patient using Clustal X 2.0 [76] . For each patient, every unique variant is identified by the NGS platform used and the number of sequences (frequency) obtained, e.g., 454#1290. For each position only those nucleotides that differ from the population sequence are depicted. Dashes indicated the same nucleotide as the population sequence while gaps introduced to maintain the alignment are indicated by dots. Relative clustering of the data from the NGS platforms was inferred by neighbor-joining, phylogenetic analyses determined using MEGA 5.05 [77] and displayed in a circle with topology only to facilitate their interpretation. Bootstrap resampling (1,000 data sets) of the multiple alignments tested the statistical robustness of the trees, with percentage values above 60% indicated by an asterisk. The size of the circles in the phylogenetic trees correlates with the frequency of the unique sequence determined by each NGS platform (color) in the logarithmic scale. The black box denotes the population (sanger) sequence for each sample.

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–65, 10–69, and 10–73 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence from the respective patient using Clustal X 2.0 [76] . For each patient, every unique variant is identified by the NGS platform used and the number of sequences (frequency) obtained, e.g., 454#1290. For each position only those nucleotides that differ from the population sequence are depicted. Dashes indicated the same nucleotide as the population sequence while gaps introduced to maintain the alignment are indicated by dots. Relative clustering of the data from the NGS platforms was inferred by neighbor-joining, phylogenetic analyses determined using MEGA 5.05 [77] and displayed in a circle with topology only to facilitate their interpretation. Bootstrap resampling (1,000 data sets) of the multiple alignments tested the statistical robustness of the trees, with percentage values above 60% indicated by an asterisk. The size of the circles in the phylogenetic trees correlates with the frequency of the unique sequence determined by each NGS platform (color) in the logarithmic scale. The black box denotes the population (sanger) sequence for each sample.

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing, Sequencing, Variant Assay

    Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–75, 10–80, and 10–91 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of the clustering of variants across platforms. The ten most common nucleotide V3 sequences from samples 10–75, 10–80, and 10–91 -obtained with each of the four NGS platforms (454™, Illumina®, PacBio®, and Ion Torrent™)- were aligned against the respective population (sanger) sequence and analyzed as described in the Figure 4 legend.

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing, Sequencing

    Comparison of the frequency of variants across NGS platforms. The heights of the bars represent the combined frequency of V3 variants detected by the NGS platforms 454™, Illumina®, PacBio®, and Ion Torrent™ prior to filtering. The colors within each bar denote the proportional contribution made by each platform after normalization based on coverage. Insets show low frequency variants up to a maximum of 20 unique sequences.

    Journal: PLoS ONE

    Article Title: Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    doi: 10.1371/journal.pone.0049602

    Figure Lengend Snippet: Comparison of the frequency of variants across NGS platforms. The heights of the bars represent the combined frequency of V3 variants detected by the NGS platforms 454™, Illumina®, PacBio®, and Ion Torrent™ prior to filtering. The colors within each bar denote the proportional contribution made by each platform after normalization based on coverage. Insets show low frequency variants up to a maximum of 20 unique sequences.

    Article Snippet: The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies).

    Techniques: Next-Generation Sequencing

    SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each NGS platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the PacBio data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.

    Journal: Nucleic Acids Research

    Article Title: Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

    doi: 10.1093/nar/gku537

    Figure Lengend Snippet: SNV calling based only on the alignment (naïve) versus haplotype reconstruction. ( A ) Distribution of SNVs across the full-length HIV-1 coding region compared to the ground truths for each NGS platform, on top shown as directly obtained from the alignment and on the bottom after gene-wise haplotype reconstruction. A SNV is called from the alignment, when its relative occurrence is higher than 1%, except for the deletions within the PacBio data, where a threshold of 5% was applied. SNVs from inferred haplotypes are called if found in at least one reconstructed haplotype. False positive SNVs and false negative SNVs are represented as upward and downward pointing bars, respectively. Bars are color coded for the four different nucleotides and the gap-symbol, bars may stack for multiple false calls at a single position, and false positives and false negatives may occur at the same position. ( B ) Co-occurrence of false positive and false negative SNVs among NGS platforms shown as Venn diagrams, with and without gene-wise haplotype reconstruction.

    Article Snippet: Three NGS technologies, namely, 454/Roche, Illumina and PacBio, were applied to sequence the full-length genomes of the mixture of HIV-1 strains, each requiring different protocols for sample preparation and sequencing.

    Techniques: Next-Generation Sequencing

    HIV-1 full-length genome sequencing using three different NGS technologies. ( A ) Experimental protocol. Five HIV-1 full-length plasmids were transfected into 293T cells to generate five different virus stocks. These clones were mixed in a large batch and aliquoted. RNA was isolated and amplified with three different protocols. DNA libraries were sequenced with either 454/Roche, Illumina or PacBio. ( B ) Coverage in overlapping reads per base pair. The map of the HIV-1 genome is shown on the top, with each subsequently analyzed gene indicated. The position numbering refers to the HIV-1 HXB2 genome (GenBank accession number K03455). Amplicon layout is visualized for each NGS platform with individual numbering (Supplementary Table S1). ( C ) Read length distribution of each NGS technology, after preprocessing and alignment.

    Journal: Nucleic Acids Research

    Article Title: Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

    doi: 10.1093/nar/gku537

    Figure Lengend Snippet: HIV-1 full-length genome sequencing using three different NGS technologies. ( A ) Experimental protocol. Five HIV-1 full-length plasmids were transfected into 293T cells to generate five different virus stocks. These clones were mixed in a large batch and aliquoted. RNA was isolated and amplified with three different protocols. DNA libraries were sequenced with either 454/Roche, Illumina or PacBio. ( B ) Coverage in overlapping reads per base pair. The map of the HIV-1 genome is shown on the top, with each subsequently analyzed gene indicated. The position numbering refers to the HIV-1 HXB2 genome (GenBank accession number K03455). Amplicon layout is visualized for each NGS platform with individual numbering (Supplementary Table S1). ( C ) Read length distribution of each NGS technology, after preprocessing and alignment.

    Article Snippet: Three NGS technologies, namely, 454/Roche, Illumina and PacBio, were applied to sequence the full-length genomes of the mixture of HIV-1 strains, each requiring different protocols for sample preparation and sequencing.

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

    Schematic diagram of our focused pulse laser radiation pressure-driven non-contact target bead sniper system. ( a ) A motorized stage moves the sequencing plate and locates the target clone bead to the focusing spot of the pulse laser based on the real-world location information from our diffusion-like local mapping algorithm. Target clone beads were isolated into a PCR tube to directly utilize sequence-verified oligonucleotides on the bead surface. ( b ) The selectively etched fibre bundle structure of the 454 NGS substrate is well suited for optical releasing. The etched core region partially isolates a single clone bead while the remnant core delivers serial optical signals of pyrosequencing to the CCD. We used biocompatible 532-nm visible light to illuminate the side opposite to the bead-containing side and to couple the core region to carry the photon energy to the target bead penetrating through the sequencing plate. A nanosecond pulse effectively exerts a radiation force to target the bead without physical damage (longer pulse) or simple locoregional ablation (shorter pulse). ( c ) Since the fibre only carries light in the core region and otherwise attenuates light, it also minimizes the horizontal and vertical positioning error. This approach allows robust clone bead targeting without expensive optical and mechanical instruments. A single pulse with energy of ~50 μJ applies 0.25 μN of radiation force for target bead retrieval.

    Journal: Nature Communications

    Article Title: A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform

    doi: 10.1038/ncomms7073

    Figure Lengend Snippet: Schematic diagram of our focused pulse laser radiation pressure-driven non-contact target bead sniper system. ( a ) A motorized stage moves the sequencing plate and locates the target clone bead to the focusing spot of the pulse laser based on the real-world location information from our diffusion-like local mapping algorithm. Target clone beads were isolated into a PCR tube to directly utilize sequence-verified oligonucleotides on the bead surface. ( b ) The selectively etched fibre bundle structure of the 454 NGS substrate is well suited for optical releasing. The etched core region partially isolates a single clone bead while the remnant core delivers serial optical signals of pyrosequencing to the CCD. We used biocompatible 532-nm visible light to illuminate the side opposite to the bead-containing side and to couple the core region to carry the photon energy to the target bead penetrating through the sequencing plate. A nanosecond pulse effectively exerts a radiation force to target the bead without physical damage (longer pulse) or simple locoregional ablation (shorter pulse). ( c ) Since the fibre only carries light in the core region and otherwise attenuates light, it also minimizes the horizontal and vertical positioning error. This approach allows robust clone bead targeting without expensive optical and mechanical instruments. A single pulse with energy of ~50 μJ applies 0.25 μN of radiation force for target bead retrieval.

    Article Snippet: PCR conditions were 10 μl 2 × p.f.u. polymerase pre-mix (Solgent, Daejeon, Korea) and 1 μl (20 μM) each primer with cycling conditions of initial denaturation at 95 °C for 3 min followed by 25 cycles of 95 °C for 30 s, 60 °C for 30 s, 72 °C for 30 s and final elongation at 72 °C for 5 min. All PCR products were analysed by both agarose gel electrophoresis and the NGS platform (Roche/454 GS Junior+).

    Techniques: Sequencing, Diffusion-based Assay, Isolation, Polymerase Chain Reaction, Next-Generation Sequencing

    False positive rates (FPRs) and false negative rates for the three NGS technologies at simulated varying coverage depths. Performances of (a) Roche 454, (b) Illumina GA, and (c) ABI SOLiD at lower coverage depths were simulated by random subsampling of the reads. Error bars represent the standard deviation over the four samples for ten iterations. The thresholds for a 10% and 50% error rate degradation of the minimum false positive rate are indicated by dashed and dotted lines, respectively, and the corresponding coverage depth reported in dashed and dotted boxes, respectively.

    Journal: Genome Biology

    Article Title: Evaluation of next generation sequencing platforms for population targeted sequencing studies

    doi: 10.1186/gb-2009-10-3-r32

    Figure Lengend Snippet: False positive rates (FPRs) and false negative rates for the three NGS technologies at simulated varying coverage depths. Performances of (a) Roche 454, (b) Illumina GA, and (c) ABI SOLiD at lower coverage depths were simulated by random subsampling of the reads. Error bars represent the standard deviation over the four samples for ten iterations. The thresholds for a 10% and 50% error rate degradation of the minimum false positive rate are indicated by dashed and dotted lines, respectively, and the corresponding coverage depth reported in dashed and dotted boxes, respectively.

    Article Snippet: Indeed, heterozygous indel detection, which is difficult using PCR-based sample preparation methods and ABI Sanger sequencing [ ], may be easier to achieve using NGS platforms because each allele is sequenced and detected independently.

    Techniques: Next-Generation Sequencing, Standard Deviation

    Overview of experimental design. Six genomic intervals, each encoding genes for K + /Na + voltage-gated channel proteins, were amplified using DNA from four individuals and LR-PCR reactions to generate 260 kb of target sequence per sample. Amplicons from each individual were pooled in equimolar amounts and then sequenced using the three NGS platforms. The 260 kb examined in this study is representative of human sequences containing 38% repeats and 4% coding sequence compared with 47% and 1%, respectively, genome-wide. For each sample 88 kb was amplified using short range PCR (SR-PCR) reactions targeting the exons and evolutionarily conserved intronic regions. Each SR-PCR amplicon was individually sequenced in the forward and reverse directions using the ABI-3730xL platform (Additional data file 2). Data generated from the NGS platforms were analyzed to identify bases variants from the reference sequence (build 36) and the quality of the variant calls was assessed using platform specific methodologies. A comparative analysis of the sequence data from the NGS platforms and ABI Sanger was then performed to determine accuracy, and false positive and false negative rates.

    Journal: Genome Biology

    Article Title: Evaluation of next generation sequencing platforms for population targeted sequencing studies

    doi: 10.1186/gb-2009-10-3-r32

    Figure Lengend Snippet: Overview of experimental design. Six genomic intervals, each encoding genes for K + /Na + voltage-gated channel proteins, were amplified using DNA from four individuals and LR-PCR reactions to generate 260 kb of target sequence per sample. Amplicons from each individual were pooled in equimolar amounts and then sequenced using the three NGS platforms. The 260 kb examined in this study is representative of human sequences containing 38% repeats and 4% coding sequence compared with 47% and 1%, respectively, genome-wide. For each sample 88 kb was amplified using short range PCR (SR-PCR) reactions targeting the exons and evolutionarily conserved intronic regions. Each SR-PCR amplicon was individually sequenced in the forward and reverse directions using the ABI-3730xL platform (Additional data file 2). Data generated from the NGS platforms were analyzed to identify bases variants from the reference sequence (build 36) and the quality of the variant calls was assessed using platform specific methodologies. A comparative analysis of the sequence data from the NGS platforms and ABI Sanger was then performed to determine accuracy, and false positive and false negative rates.

    Article Snippet: Indeed, heterozygous indel detection, which is difficult using PCR-based sample preparation methods and ABI Sanger sequencing [ ], may be easier to achieve using NGS platforms because each allele is sequenced and detected independently.

    Techniques: Amplification, Polymerase Chain Reaction, Sequencing, Next-Generation Sequencing, Genome Wide, Generated, Variant Assay

    Each NGS technology generates a consistent pattern of non-uniform sequence coverage. (a) Sequence coverage depth is displayed as a gray-scale (0-100× for Roche 454; 0-500× for Illumina GA and ABI SOLiD) along an approximately 25-kb region of chromosome 11 amplified by three long-range PCR products (red rectangles). (b) A heat-map colored matrix displays the coefficient of correlation of coverage across the entire 260 kb of analyzed sequence between each of the 72 possible pair-wise comparisons (four samples by three technologies). The apparent lower correlation of the Roche-454 sequence coverage is more reflective of the smaller amplitude in the coverage variability (lower average coefficient of variance) than a lack of coverage correlation from sample to sample. The correlation of NA17460 with the other three samples on the ABI SOLiD platform is slightly lower due to technological issues (Additional data file 2) and was therefore excluded from the coefficient of correlation calculation reported in the text.

    Journal: Genome Biology

    Article Title: Evaluation of next generation sequencing platforms for population targeted sequencing studies

    doi: 10.1186/gb-2009-10-3-r32

    Figure Lengend Snippet: Each NGS technology generates a consistent pattern of non-uniform sequence coverage. (a) Sequence coverage depth is displayed as a gray-scale (0-100× for Roche 454; 0-500× for Illumina GA and ABI SOLiD) along an approximately 25-kb region of chromosome 11 amplified by three long-range PCR products (red rectangles). (b) A heat-map colored matrix displays the coefficient of correlation of coverage across the entire 260 kb of analyzed sequence between each of the 72 possible pair-wise comparisons (four samples by three technologies). The apparent lower correlation of the Roche-454 sequence coverage is more reflective of the smaller amplitude in the coverage variability (lower average coefficient of variance) than a lack of coverage correlation from sample to sample. The correlation of NA17460 with the other three samples on the ABI SOLiD platform is slightly lower due to technological issues (Additional data file 2) and was therefore excluded from the coefficient of correlation calculation reported in the text.

    Article Snippet: Indeed, heterozygous indel detection, which is difficult using PCR-based sample preparation methods and ABI Sanger sequencing [ ], may be easier to achieve using NGS platforms because each allele is sequenced and detected independently.

    Techniques: Next-Generation Sequencing, Sequencing, Amplification, Polymerase Chain Reaction

    Performance metrics of NGS technologies. (a-f) Error bars represent minimum and maximum values obtained from the four samples. (g-i) Venn diagram representation of false positive calls (g), false negative calls (h) and discrepant variants calls (i). The inset caption displays the color-coding of each NGS technology and overlaps: for Roche 454 (red), Illumina GA (yellow) and ABI SOLiD (blue). For each NGS platform the number of base calls with errors associated with specific sequence contexts is given (repeat = repetitive element). When two sequence contexts are present they are both listed.

    Journal: Genome Biology

    Article Title: Evaluation of next generation sequencing platforms for population targeted sequencing studies

    doi: 10.1186/gb-2009-10-3-r32

    Figure Lengend Snippet: Performance metrics of NGS technologies. (a-f) Error bars represent minimum and maximum values obtained from the four samples. (g-i) Venn diagram representation of false positive calls (g), false negative calls (h) and discrepant variants calls (i). The inset caption displays the color-coding of each NGS technology and overlaps: for Roche 454 (red), Illumina GA (yellow) and ABI SOLiD (blue). For each NGS platform the number of base calls with errors associated with specific sequence contexts is given (repeat = repetitive element). When two sequence contexts are present they are both listed.

    Article Snippet: Indeed, heterozygous indel detection, which is difficult using PCR-based sample preparation methods and ABI Sanger sequencing [ ], may be easier to achieve using NGS platforms because each allele is sequenced and detected independently.

    Techniques: Next-Generation Sequencing, Sequencing