amplicons Search Results


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  • 94
    Pacific Biosciences amplicons
    Categories of sequencing reads inferred from the PacBio NGS sequencing. (A) Categories of sequencing reads deriving from the gapC amplicon, (B) i6-tubA amplicon and (C) i5-tubA amplicon, respectively. Number and percentage of particular types of reads are given. The distribution of introns in all groups of reads is depicted. Lines represent the exons while circles represent the introns: black circles: conventional introns; white: nonconventional ones (not to scale). Introns are labelled i1 –i6. In addition, introns that exhibit intermediate features are marked with an asterisk. Double asterisk indicates the introns to which the reverse primer was targeted, thus not considered in the analysis of <t>amplicons</t> (introns to which primers annealed were inevitably present in the amplification products).
    Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 677 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    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: 94/100, based on 7242 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher amplicons
    Engineered cycloheximide resistance establishes genome editing conditions. ( A ) The design of a cycloheximide resistant allele, rpl36a P56Q , in S. rosetta . The protospacer adjacent motif (PAM, orange) next to the 56 th codon of rpl36a (Target, cyan), which is located on the second exon (thick black line labeled 2), provides a suitable site to design a gRNA that targets Sp Cas9 cleavage (sequence is shown underneath the locus schematic, and carets indicate the target cleavage site). A repair oligonucleotide (black line with knob) introduces a cycloheximide resistant allele, rpl36a P56Q (Mutation, purple), flanked by 100 bases of homologous sequence. The sequence of the edited allele is shown below. ( B–D ) A comparison of genotypes from populations of unedited cells ( B ), edited cells ( C ), and a strain established from a clonal isolate of edited cells ( D ) shows that cycloheximide selection enriches for rpl36a P56Q . The genotype for each population was determined by amplifying the locus with primers surrounding the editing site (black arrows in panel A) that did not overlap in sequence with the repair oligonucleotide. One of the primers had a T3 primer binding site for Sanger sequencing of <t>amplicons</t> (black arrow with flap). Remarkably, after selection, the wild-type allele was not detected ( B ). ( E ) S. rosetta uses repair oligonucleotides with > 20 nt homology arms for genome editing. Truncations of repair oligonucleotides encoding the rpl36a P56Q allele were designed in the same orientation as gRNAs (sense, black dots and lines) or the opposite orientation (antisense, gray dots and lines). 24 hr after S. rosetta recovered from transfections with repair templates and Sp Cas9 RNPs, cycloheximide was added to grow cells in selective media for five days, at which time the cells were harvested for counting cell density and for genotyping. Closed circles indicate that the consensus genotype of the cell population had the rpl36a P56Q allele in Sanger sequencing; whereas, open circles indicate that the cell population had the wild-type allele. E’ and E’’ show two independent trials. Notably, we observed a slight bias for repair oligonucleotides in the sense direction, particularly with shorter homology arms of 20-30 bases. Because repair templates in the sense orientation with 40–80 bases of homologous sequence resulted in the best editing, we performed subsequent optimization with a sense repair oligonucleotide that 50-base homology arms on each side of the double-stranded break. ( F ) Small quantities of Sp Cas9 RNPs are sufficient to initiate genome editing. Decreasing concentrations of Sp Cas9 RNP ( Sp Cas9 was the limiting factor) and a constant amount of repair template were transfected into S. rosetta . After characterizing genome editing outcomes by counting cell density and sequencing the consensus genotype (described in panel E), we found that low concentrations of Sp Cas9 (20 pmol) were sufficient to introduce the rpl36a P56Q allele. F’ and F’’ show two independent trials. ( G ) High concentrations of repair oligonucleotides increase genome editing efficiency. A serial dilution of a repair template was delivered into S. rosetta . The cell density and consensus genotypes from these experiments show that all concentrations of repair template can introduce the rpl36a P56Q allele, but the higher cell densities recovered after transfection with increasing concentrations of repair templates indicate more efficient editing. G’ and G’’ show two independent trials. ( H ) The addition of gRNAs stimulates genome editing. Genome editing was performed by delivering a repair oligonucleotide with Sp Cas9 without the addition of any gRNA or with a gRNA that was prepared from in vitro transcriptions (noted as gRNA in figure) or with a synthetic crRNA that was annealed to a synthetic tracrRNA (noted as crRNA). The consensus genotype and cell densities from these experiments show that gRNAs are necessary for editing and that gRNAs from either source were sufficient for editing. The dots show two independent experiments and lines show their average result.
    Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 51859 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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: 92/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc amplicons
    Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small <t>amplicons)</t> were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.
    Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 16822 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    LGC Genomics GmbH amplicons
    Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small <t>amplicons)</t> were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.
    Amplicons, supplied by LGC Genomics GmbH, used in various techniques. Bioz Stars score: 92/100, based on 250 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Advanced Analytical Inc amplicons
    Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small <t>amplicons)</t> were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.
    Amplicons, supplied by Advanced Analytical Inc, used in various techniques. Bioz Stars score: 92/100, based on 187 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Macrogen amplicons
    Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small <t>amplicons)</t> were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.
    Amplicons, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 2133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eurofins amplicons
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 94/100, based on 1138 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    MWG-Biotech amplicons
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Amplicons, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 92/100, based on 102 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Bio-Rad amplicon detection
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Amplicon Detection, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 89/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche amplicon resequencing
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Amplicon Resequencing, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Kaneka Corp control amplicon
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Control Amplicon, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Bioneer Corporation rassf1a amplicons
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    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
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    88
    Illumina Inc truseq amplicon
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Truseq Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc truseqcustom amplicon
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Truseqcustom Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche amplicon a kit
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Amplicon A Kit, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Sigma-Genosys cygb amplicon
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    Cygb Amplicon, supplied by Sigma-Genosys, used in various techniques. Bioz Stars score: 85/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher v6 amplicons
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    V6 Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore amplicon filters
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
    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
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    Genewiz amplicon identity
    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent <t>amplicons</t> are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
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    Image Search Results


    Categories of sequencing reads inferred from the PacBio NGS sequencing. (A) Categories of sequencing reads deriving from the gapC amplicon, (B) i6-tubA amplicon and (C) i5-tubA amplicon, respectively. Number and percentage of particular types of reads are given. The distribution of introns in all groups of reads is depicted. Lines represent the exons while circles represent the introns: black circles: conventional introns; white: nonconventional ones (not to scale). Introns are labelled i1 –i6. In addition, introns that exhibit intermediate features are marked with an asterisk. Double asterisk indicates the introns to which the reverse primer was targeted, thus not considered in the analysis of amplicons (introns to which primers annealed were inevitably present in the amplification products).

    Journal: PLoS Genetics

    Article Title: Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis

    doi: 10.1371/journal.pgen.1007761

    Figure Lengend Snippet: Categories of sequencing reads inferred from the PacBio NGS sequencing. (A) Categories of sequencing reads deriving from the gapC amplicon, (B) i6-tubA amplicon and (C) i5-tubA amplicon, respectively. Number and percentage of particular types of reads are given. The distribution of introns in all groups of reads is depicted. Lines represent the exons while circles represent the introns: black circles: conventional introns; white: nonconventional ones (not to scale). Introns are labelled i1 –i6. In addition, introns that exhibit intermediate features are marked with an asterisk. Double asterisk indicates the introns to which the reverse primer was targeted, thus not considered in the analysis of amplicons (introns to which primers annealed were inevitably present in the amplification products).

    Article Snippet: The amplicons obtained as a result of RT-PCR reactions for the gapC and tubA genes were sequenced commercially in the Museum and Institute of Zoology of the Polish Academy of Science, Warsaw, Poland, on the PacBio RS II (Pacific Biosciences) instrument.

    Techniques: Sequencing, Next-Generation Sequencing, Amplification

    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

    Engineered cycloheximide resistance establishes genome editing conditions. ( A ) The design of a cycloheximide resistant allele, rpl36a P56Q , in S. rosetta . The protospacer adjacent motif (PAM, orange) next to the 56 th codon of rpl36a (Target, cyan), which is located on the second exon (thick black line labeled 2), provides a suitable site to design a gRNA that targets Sp Cas9 cleavage (sequence is shown underneath the locus schematic, and carets indicate the target cleavage site). A repair oligonucleotide (black line with knob) introduces a cycloheximide resistant allele, rpl36a P56Q (Mutation, purple), flanked by 100 bases of homologous sequence. The sequence of the edited allele is shown below. ( B–D ) A comparison of genotypes from populations of unedited cells ( B ), edited cells ( C ), and a strain established from a clonal isolate of edited cells ( D ) shows that cycloheximide selection enriches for rpl36a P56Q . The genotype for each population was determined by amplifying the locus with primers surrounding the editing site (black arrows in panel A) that did not overlap in sequence with the repair oligonucleotide. One of the primers had a T3 primer binding site for Sanger sequencing of amplicons (black arrow with flap). Remarkably, after selection, the wild-type allele was not detected ( B ). ( E ) S. rosetta uses repair oligonucleotides with > 20 nt homology arms for genome editing. Truncations of repair oligonucleotides encoding the rpl36a P56Q allele were designed in the same orientation as gRNAs (sense, black dots and lines) or the opposite orientation (antisense, gray dots and lines). 24 hr after S. rosetta recovered from transfections with repair templates and Sp Cas9 RNPs, cycloheximide was added to grow cells in selective media for five days, at which time the cells were harvested for counting cell density and for genotyping. Closed circles indicate that the consensus genotype of the cell population had the rpl36a P56Q allele in Sanger sequencing; whereas, open circles indicate that the cell population had the wild-type allele. E’ and E’’ show two independent trials. Notably, we observed a slight bias for repair oligonucleotides in the sense direction, particularly with shorter homology arms of 20-30 bases. Because repair templates in the sense orientation with 40–80 bases of homologous sequence resulted in the best editing, we performed subsequent optimization with a sense repair oligonucleotide that 50-base homology arms on each side of the double-stranded break. ( F ) Small quantities of Sp Cas9 RNPs are sufficient to initiate genome editing. Decreasing concentrations of Sp Cas9 RNP ( Sp Cas9 was the limiting factor) and a constant amount of repair template were transfected into S. rosetta . After characterizing genome editing outcomes by counting cell density and sequencing the consensus genotype (described in panel E), we found that low concentrations of Sp Cas9 (20 pmol) were sufficient to introduce the rpl36a P56Q allele. F’ and F’’ show two independent trials. ( G ) High concentrations of repair oligonucleotides increase genome editing efficiency. A serial dilution of a repair template was delivered into S. rosetta . The cell density and consensus genotypes from these experiments show that all concentrations of repair template can introduce the rpl36a P56Q allele, but the higher cell densities recovered after transfection with increasing concentrations of repair templates indicate more efficient editing. G’ and G’’ show two independent trials. ( H ) The addition of gRNAs stimulates genome editing. Genome editing was performed by delivering a repair oligonucleotide with Sp Cas9 without the addition of any gRNA or with a gRNA that was prepared from in vitro transcriptions (noted as gRNA in figure) or with a synthetic crRNA that was annealed to a synthetic tracrRNA (noted as crRNA). The consensus genotype and cell densities from these experiments show that gRNAs are necessary for editing and that gRNAs from either source were sufficient for editing. The dots show two independent experiments and lines show their average result.

    Journal: eLife

    Article Title: Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta

    doi: 10.7554/eLife.56193

    Figure Lengend Snippet: Engineered cycloheximide resistance establishes genome editing conditions. ( A ) The design of a cycloheximide resistant allele, rpl36a P56Q , in S. rosetta . The protospacer adjacent motif (PAM, orange) next to the 56 th codon of rpl36a (Target, cyan), which is located on the second exon (thick black line labeled 2), provides a suitable site to design a gRNA that targets Sp Cas9 cleavage (sequence is shown underneath the locus schematic, and carets indicate the target cleavage site). A repair oligonucleotide (black line with knob) introduces a cycloheximide resistant allele, rpl36a P56Q (Mutation, purple), flanked by 100 bases of homologous sequence. The sequence of the edited allele is shown below. ( B–D ) A comparison of genotypes from populations of unedited cells ( B ), edited cells ( C ), and a strain established from a clonal isolate of edited cells ( D ) shows that cycloheximide selection enriches for rpl36a P56Q . The genotype for each population was determined by amplifying the locus with primers surrounding the editing site (black arrows in panel A) that did not overlap in sequence with the repair oligonucleotide. One of the primers had a T3 primer binding site for Sanger sequencing of amplicons (black arrow with flap). Remarkably, after selection, the wild-type allele was not detected ( B ). ( E ) S. rosetta uses repair oligonucleotides with > 20 nt homology arms for genome editing. Truncations of repair oligonucleotides encoding the rpl36a P56Q allele were designed in the same orientation as gRNAs (sense, black dots and lines) or the opposite orientation (antisense, gray dots and lines). 24 hr after S. rosetta recovered from transfections with repair templates and Sp Cas9 RNPs, cycloheximide was added to grow cells in selective media for five days, at which time the cells were harvested for counting cell density and for genotyping. Closed circles indicate that the consensus genotype of the cell population had the rpl36a P56Q allele in Sanger sequencing; whereas, open circles indicate that the cell population had the wild-type allele. E’ and E’’ show two independent trials. Notably, we observed a slight bias for repair oligonucleotides in the sense direction, particularly with shorter homology arms of 20-30 bases. Because repair templates in the sense orientation with 40–80 bases of homologous sequence resulted in the best editing, we performed subsequent optimization with a sense repair oligonucleotide that 50-base homology arms on each side of the double-stranded break. ( F ) Small quantities of Sp Cas9 RNPs are sufficient to initiate genome editing. Decreasing concentrations of Sp Cas9 RNP ( Sp Cas9 was the limiting factor) and a constant amount of repair template were transfected into S. rosetta . After characterizing genome editing outcomes by counting cell density and sequencing the consensus genotype (described in panel E), we found that low concentrations of Sp Cas9 (20 pmol) were sufficient to introduce the rpl36a P56Q allele. F’ and F’’ show two independent trials. ( G ) High concentrations of repair oligonucleotides increase genome editing efficiency. A serial dilution of a repair template was delivered into S. rosetta . The cell density and consensus genotypes from these experiments show that all concentrations of repair template can introduce the rpl36a P56Q allele, but the higher cell densities recovered after transfection with increasing concentrations of repair templates indicate more efficient editing. G’ and G’’ show two independent trials. ( H ) The addition of gRNAs stimulates genome editing. Genome editing was performed by delivering a repair oligonucleotide with Sp Cas9 without the addition of any gRNA or with a gRNA that was prepared from in vitro transcriptions (noted as gRNA in figure) or with a synthetic crRNA that was annealed to a synthetic tracrRNA (noted as crRNA). The consensus genotype and cell densities from these experiments show that gRNAs are necessary for editing and that gRNAs from either source were sufficient for editing. The dots show two independent experiments and lines show their average result.

    Article Snippet: After quantifying DNA (Qubit; Thermo Fisher Scientific) and pooling equimolar amounts of sample, the amplicons were further purified with magnetic beads (UC Berkeley Functional Genomics Lab) and the concentration was verified using qPCR.

    Techniques: Labeling, Sequencing, Mutagenesis, Selection, Binding Assay, Transfection, Introduce, Serial Dilution, In Vitro

    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

    Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small amplicons) were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.

    Journal: Scientific Reports

    Article Title: Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing

    doi: 10.1038/s41598-017-10591-9

    Figure Lengend Snippet: Tag-linkage sequencing of HBV RT/S region. ( a ) A schematic presentation of the HBV viral genome region (polymerase gene) that was processed and reconstructed using the tag-linkage method. 836 bp of polymerase gene (blue box) was recovered, including the majority of the reverse transcriptase domain (overlapping S gene) and part of the RNase H gene. ( b ) A schematic presentation of the experiment flow for tag linkage deep sequencing. 1) HBV sequences were amplified from viral DNA extracted from patient plasma using primers targeting conserved region. Tags were added onto each molecule for sequencing error correction and haplotype reconstruction. 2) Different length of sequences (covering different number of non-overlapping small amplicons) were amplified from ~10,000 molecules. 3) Amplified sequences were ligated. 4) Small amplicons were further amplified for sequencing.

    Article Snippet: Finally, sequencing adaptors were added onto amplicons for Illumina sequencing.

    Techniques: Sequencing, Flow Cytometry, Amplification

    Results of the experimentally determined composition of the MOCK Community (MC) at ( a ) family and ( b ) genus level with MinION and Illumina NGS techniques. The results are based on 16S rRNA amplicon sequencing. Experimentally determined 16S rRNA gene percentage abundance are compared against the actual composition of the MC as reported by the supplier (i.e. Zymo Research). Data points are an average of duplicate samples for Illumina and triplicate samples for MinION sequencing. Error bars indicate the standard deviation.

    Journal: Scientific Reports

    Article Title: A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

    doi: 10.1038/s41598-019-51997-x

    Figure Lengend Snippet: Results of the experimentally determined composition of the MOCK Community (MC) at ( a ) family and ( b ) genus level with MinION and Illumina NGS techniques. The results are based on 16S rRNA amplicon sequencing. Experimentally determined 16S rRNA gene percentage abundance are compared against the actual composition of the MC as reported by the supplier (i.e. Zymo Research). Data points are an average of duplicate samples for Illumina and triplicate samples for MinION sequencing. Error bars indicate the standard deviation.

    Article Snippet: The amplicon data from Illumina were processed using an open source software package: Quantitative Insights Into Microbial Ecology, QIIME 2 ( https://qiime2.org/ ).

    Techniques: Next-Generation Sequencing, Amplification, Sequencing, Standard Deviation

    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

    The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent amplicons are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).

    Journal: Genome Biology and Evolution

    Article Title: Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii

    doi: 10.1093/gbe/evu119

    Figure Lengend Snippet: The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent amplicons are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).

    Article Snippet: Amplicons were sequenced by MWG-Eurofins France.

    Techniques: Binding Assay, Polymerase Chain Reaction, Amplification