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  • 95
    Illumina Inc amplicons
    Agilent TapeStation 4200 results of RNA fragementation using High Sensitivity RNA ScreenTape. A small aliquot of total RNA (2μg) was fragemented for various durations at 70C and then a highly-diluted sample (~3ng/μL) was analyzed according to the manufacturer’s protocol. A) Example of over-fragmented sample that is outside the recommended range of 100-200bp (9 min of fragmentation). B) Optimal fragmentation result (~3 min). C) Under fragmented sample (1 min with higher concentration); although minimal under-fragmenation will likely still yield acceptable libraries, more extreme scenarios such as the one depicted will result in large <t>amplicons</t> that are outside the recommended range of the sequencer. “Lower” refers to the lower size marker for the TapeStation instrument.
    Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 17327 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc amplicon sequencing
    Phylogeny of 34 most abundant operational taxonomic units (OTUs) of ur e C (corresponding to the species level). ur e C reads obtained by <t>amplicon</t> sequencing on the Illumina MiSeq platform were clustered into species-level OTUs with ≥91% sequence identity, and a phylogenetic tree was constructed by the maximum likelihood method with the Jones-Taylor-Thornton model by means of the ur e C sequence of Canavalia ensiformis (M65260) as an outgroup. Branching points that support probability > 80% in the bootstrap analyses (based on 500 replicates) are shown as filled circles. The heatmap shows the relative abundance of species-level OTUs of ure C in soil samples 1 to 7. The scale bar represents 20% sequence divergence. Nucleotide sequence accession numbers are indicated in parentheses.
    Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 3293 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc amplicon libraries
    Experimental design. ( a ) Design of single and dual-index sequencing strategy and schematic describing the 3 <t>amplicon</t> designs: Fusion Primer Design (A) is a one step PCR which uses a single 12-nt error-correcting Golay index sequence (blue) allowing a high multiplexing capability. Tag tailed design (B) is a 2-step PCR which uses a universal primer for the first step and a dual index barcoded primer set in the second step. Standard Illumina Nextera 8-nt index sequences were used (pink Index 5; blue Index 7). The Pac Bio Ligate Adapters design (C): Two harpin adapters (grey) were ligated to a barcoded template (BF forward barcode; BR reverse barcode) to allow multiplexing. ( b ) Platform Specific Amplicon Libraries: Illumina paired-end sequencing (1,2) generates 2 sequencing reads (R1 and R2) per each cluster and can have single (Standard/Golay) or dual indexes (I5, I7). Ion Torrent and 454 (3) have a single read for each bead with a single index (MID). Pacific Bioscience generate a single circular read for each molecule (SMRT bell) and can have one (BF or BR) or two indexes. The starting point and direction of sequencing reads are indicated by a solid blue line and arrows, respectively. In the case of Fusion Primer Design custom sequencing primer were used
    Amplicon Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 1866 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies amplicons
    Genome browser shot (hg19) illustrating the HAM-TBS FKBP5 panel and important locus-specific data. CTCF -ChIA-PET : track indicating the locations of CTCF ]). CTCF ChIP-seq and GR Chip-seq : regions of transcription factor binding derived from chromatin immunoprecipitation (ChIP) experiments in multiple cell lines from the ENCODE project; HAM-TBS FKBP5 panel : locations of the <t>amplicons</t> contained in this panel
    Amplicons, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 3253 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Macrogen amplicons
    Induction of HCV escape from a direct acting antiviral in HFBR. ( a ) Timeline of Huh7.5 cell cultivation in DMEM + 10%FBS and serum-free AEM, indicating infection with HCV and initiation of treatment with different concentrations of the NS5A inhibitor daclatasvir (DCV). HCV from HFBR harvests (1000 μL, 50 μL or 5 μL) were used for infection of 10 6 Huh7.5 cells plated the previous day in T25 cell culture flasks (derived cultures). Peak infectivity titers in derived cultures are reported. Amino acid at NS5A position 93 according to the H77 reference sequence (GenBank accession no AF009606) was determined by Sanger sequencing for selected harvests and derived cultures. *, H at position 93 was present in ~50% of viral genomes. ( b ) 8 × 10 7 Huh7.5 cells were seeded in a hollow fiber bioreactor in DMEM + 10% FBS and infected with 1.25 × 10 6 FFU of HCV third passage stock on day 5 post cell seeding, when glucose consumption was 590 mg/day (arrow). At day 9 post cell seeding DMEM was replaced with serum-free AEM. Treatment with daclatasvir at 7.8 nM (corresponding to 64 x EC50 29 ) was initiated at day 27 post cell seeding; at day 45 the concentration was increased to 124.2 nM (corresponding to 1024 x EC50). On day 59 the treatment was terminated. ( c and d ) Determination of HCV infectivity titers and HCV RNA titers were carried out as described in Fig. 2 . *, indicates HCV infectivity titers below assay detection level. ( e ) HCV from harvest 9, 12 and 16 were loaded on 10–40% iodixanol gradients. Following ultracentrifugation 18 fractions were collected as in Fig. 5 . HCV infectivity and HCV RNA titers of each fraction were determined as described for Fig. 2 . ( f ) RNA extracted from harvest 9, 12 and 14 at 1-, 10-, 100- and 1000-fold dilution was used for RT-PCR for generation of a full-length amplicon spanning the complete HCV ORF. PCR products were visualized on a 1% agarose gel including a 1 kb DNA ladder; expected positions of full-length <t>amplicons</t> are indicated by arrows. Gel image was cropped as indicated by boxes; full-length gel is presented in Supplementary Fig. S4 .
    Amplicons, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 2133 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc pcr amplicons
    Imprinted chromatin as a model system to quantify epigenetic influences on genome editing. (A) Schematic outlining the experimental workflow. Throughout the text, F1 hybrid cell lines are depicted with the maternal strain denoted before the paternal strain (i.e., In B×J: B is maternal and J paternal). sgRNAs are designed to cleave approximately 40–100 bp from a heterozygous SNP within imprinted chromatin (open and closed circles). MiSeq <t>amplicons</t> span both the SNP and site of mutation, which allows simultaneous assessment of genome editing outcome and parental allele at high-throughput. (B) Top: schematic showing the imprinted mouse Kcnq1 gene including H3K9me3 ChIP and DNase-I–seq data from mESCs available through EncODE (ENCSR000CFZ, GSM1014187) (bottom). Higher-resolution view of the KvDMR imprinted CpG island within Kcnq1 , showing the position of three sgRNAs used in panel E. (C) Allele-specific enrichment of H3K9me3 and H4K20me3. <t>PCR</t> fragments spanning the target sites of sgKvDMR#2 and #3 were amplified from input, or ChIP DNA prior to Sanger sequencing across an allelic SNP. gDNA = genomic DNA from purebred mice. (D) Example of CpG methylation data from the KvDMR . ChIP, chromatin immunoprecipitation; gDNA, genomic DNA; HDR, homology-directed repair; mESC, mouse embryonic stem cell, NHEJ, nonhomologous end joining; sgRNA, single guide RNA; SNP, single nucleotide polymorphism; SRA, Sequence Read Archive; ssODN, single-stranded oligodeoxynucleotide.
    Pcr Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 2213 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad amplicons
    qChIP analysis of Cib1 binding to the pit1/2 - and tin1-1 -promoter. (A) Schematic overview of promoter organization and probe regions used for qChIP experiments. Sequence of the predicted Cib1 binding sites (UPRE) in the pit1/2 and tin1-1 promoter region is given in bold in case of identical nucleotides in pit1/2 and tin1-1 UPREs. (B) qChIP analysis of Cib1 binding to the pit1/2 and tin1-1 promoter in strain SG200 cib1-3xHA 3 h after DTT (3 mM) treatment. The HA-tagged Cib1 protein was immunoprecipitated with anti HA-antibody coupled agarose beads (Sigma). Enrichment of immunoprecipitated DNA is shown relative to the input control. <t>PCR-amplicons</t> corresponding to the pit1/2 and tin1-1 promoter are significantly enriched compared to ORF controls. No significant enrichment was observed for PCR-amplicons corresponding to pit1 , pit2 and tin1-1 ORFs in comparison to the eIF2b control. Given are the mean values of four independent experiments. Error bars represent the standard error (SE). Statistical significance was tested using Student's t -test. *indicates p-value
    Amplicons, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 3401 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher amplicons
    rb1 mutant alleles and allele frequencies in somatic, germline, and tumor tissues from adult genetic mosaic zebrafish. ( a ) 14 different indel alleles in rb1 exon 2 were identified in retina, muscle, and germline genomic DNA from two adults. Mutant alleles represented 33% of cloned <t>amplicons.</t> In tumor tissue 8 unique alleles were identified, representing 87% of cloned amplicons. ( b ) Two frameshift alleles that delete 11 bp and 19 bp in rb1 exon 3 were detected in two adults. 10% of sequenced clones were mutant in retina, muscle or germline tissue. In tumor tissue 68% of sequenced clones were mutant alleles. Red arrows mark TALEN cut site.
    Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 51844 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc 16s rrna gene amplicons
    Neighbor-joining tree based on <t>16S</t> <t>rRNA</t> gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.
    16s Rrna Gene Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 667 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    MACHEREY NAGEL amplicons
    C57BL/6- Prnp ZH3/ZH3 mice do not have TALEN off-target cleavage sites. T7 endonuclease I digestion of PCR products generated from predicted OTs ( Table S1 ) and Prnp as a digestion positive control. Analyses were performed on the founder Prnp WT/ZH3 mouse and one control C57BL/6J mouse. Before enzymatic digestion, <t>amplicons</t> were subjected to a temperature gradient enabling the formation of heteroduplexes in the presence of heterozygous mutations in the amplified gDNA. In the presence of TALEN-induced mutations, fragments of the size indicated below the gels are expected to appear, in addition to the undigested, WT amplicon. Nonconsecutive lanes from the same gel show Prnp amplicon as a control. Only in the founder Prnp WT/ZH3 mouse T7 endonuclease I digestion of the Prnp amplicon results in the formation of the two predicted fragments (indicated by an asterisk).
    Amplicons, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 94/100, based on 1498 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eurofins amplicons
    Comparison of selected treatments on the visualization of RPA-generated <t>amplicons.</t> a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide
    Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 94/100, based on 1135 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad pcr amplicons
    <t>PCR-single-strand</t> conformational polymorphism of the ovine IGF-1 gene. <t>Amplicons</t> were electrophoresed on a 12% non-denaturing acrylamide/bis-acrylamide gel; 200 V, 4 °C for 12 h. Three SSCP patterns, GG, AA and GA were detected.
    Pcr Amplicons, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 1143 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc truseq amplicon cancer panel
    Oncoprint visualizing the gene mutation status of APC , KRAS , NRAS , BRAF , PIK3CA , TP53 , FBXW7 and SMAD4 assessed by <t>TruSeq</t> <t>Amplicon</t> Cancer Panel TSACP analysis for stage II ( n = 29) and stage III ( n = 31) colon cancers The rows indicate the gene mutation status of the 60 samples (grey bars) and the black spots depict mutations.
    Truseq Amplicon Cancer Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Pacific Biosciences amplicons
    Primer design (A) and quality control presequencing (B) and postsequencing (C) . (A) Primers designed on the phagemid vector and used for single chain fragment variable (scFv) PCR amplification. The scFv (VH-LINKER-VL) length range is between ~720 and ~800 bp [variable heavy (VH) between ~350 and ~400 bp and variable light (VL) between ~320 and ~350 bp]. The linker is 53 bp including the EcoRI and XbaI sites. The PCR products are expected to be ~1,000 bp on average, including the 5′ and 3′ region and the primers. (B) Agarose gel electrophoresis of PCR products. The DNA was amplified from the AAR3 fraction and PCR products were analyzed on 1.2% (w/v) agarose gel. The band at ~1,000 bp corresponds to the expected size for scFv <t>amplicons.</t> S1, S2, S3, and S4 correspond to the samples 1, 2, 3, and 4, respectively. The Bioanalyzer trace of the four samples shows the purity of amplicons with a high-quality single peak. (C) Pacific Biosciences RS II CCS2 read length distribution using P6-C4 chemistry for 1 SMRT cell (similar results were obtained for the 15 SMRT cells). Data are based on a 1-kb size-selected scFv library using a 6 h movie.
    Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 677 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Genewiz amplicons
    Generation and characterization of MISTR1 KO A549 cells. A) CRISPR/CAS deletion strategy for MISTR1 . Scissors indicate relative locations of guide RNAs designed to target sequences flanking exon 2 of this gene. The exon 2 deletion strategy was employed for ease of genotyping. Gene structure from UCSC genome browser. Sequences of breakpoints identified a 225bp deletion that included exon 2. Note identical repaired breakpoints were recovered for both clones. B) Agarose gel resolving <t>amplicons</t> from genotyping PCR of A549 KO clones. C) Western blot analysis using lysates from WT and MISTR1 KO clones. D) Measurement of proliferation rates using IncuCyte for MISTR1 KO A549 cell line. Changes in % confluence were used as a surrogate marker of cell proliferation. Data represent means ± SD (n=6 replicates). E) Western blot analysis of cleaved PARP levels using lysates from WT and MISTR1 KO cells following 16 hours of STS treatment. Densitometry analysis of PARP levels was performed using Image Lab version 6.0.1 (Bio-Rad). % Cleaved PARP= (cleaved PARP/(Full + Cleaved PARP)) * 100. STS - staurosporine.
    Amplicons, supplied by Genewiz, used in various techniques. Bioz Stars score: 94/100, based on 710 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Stratagene amplicons
    A. PCR <t>amplicons</t> generated from primer pair 11 in 9 plant species . Fa – Fragaria × ananassa /Rosaceae, Pp – Prunus persica /Rosaceae, At – Arabidopsis thaliana /Crucifereae, Cs – Citrus sinensis /Rutaceae, Ch – Coleus hybrida /Lamiaceae, Nt – Nicotiana tabacum /Solanaceae, Le – Lycopersicon esculentum /Solanaceae, Ls – Lactuca sativa /Asteraceae, Ah – Amaranthus hypochondriacus /Caryophyllaceae. B . Schematic representation of the polymorphism between the amplicons generated from primer pair 11 in tobacco, tomato and amaranthus.
    Amplicons, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 823 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc 16s rrna amplicon sequencing
    Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the <t>16S</t> <t>rRNA</t> V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.
    16s Rrna Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 452 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Biotium amplicons
    Silencing of KLK6 expression in FaDu cells promotes tumor cell proliferation. ( A ) KLK6 expression in human HNSCC (FaDu, Cal27, SCC25) and HeLa cervix carcinoma cells was monitored on protein level by Western blot analysis with cell culture supernatants (upper panel), and on transcript level by semi-quantitative (middle panels) as well as quantitative RT-PCR (lower graph). Detection of LMNB1 <t>amplicons</t> served as control for cDNA quality and quantity for semi-quantitative RT-PCR (lower panel), while transcript levels of three independent reference genes ( ACTB, LMNB1, TBP ) were used for quantitative RT-PCR data. ( B ) KLK6 expression in stable FaDu-Mock and FaDu-shKLK6 clones is given by semi-quantitative (upper panel) and quantitative RT-PCR (lower graph) and was determined as described in ( A ). Differences in tumor cell proliferation between stable FaDu-Mock and FaDu-shKLK6 clones was monitored by quantification of cell counts over a time period of six days ( C ) and a BrdU incorporation assay ( D ). The graph represents mean values and standard deviations (SD) of the percentage total of BrdU-positive cells from three independent FaDu-shKLK6 clones and mock controls, respectively
    Amplicons, supplied by Biotium, used in various techniques. Bioz Stars score: 92/100, based on 1146 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc 16s rrna gene amplicon sequencing
    Maximum-likelihood tree of <t>16S</t> <t>rRNA</t> gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.
    16s Rrna Gene Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 393 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc miseq amplicon sequencing
    Maximum likelihood tree with 200 bootstrap replicates for Papilio 5’ invected . Papilio dardanus individuals are represented by haplotypes from <t>MiSeq</t> <t>amplicon</t> sequencing. Note that P. demodocus and P. memnon are paraphyletic. Blue dots indicate nodes with bootstrap support > 70%. Bootstrap support at intraspecific nodes is not presented.
    Miseq Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 316 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Agilent TapeStation 4200 results of RNA fragementation using High Sensitivity RNA ScreenTape. A small aliquot of total RNA (2μg) was fragemented for various durations at 70C and then a highly-diluted sample (~3ng/μL) was analyzed according to the manufacturer’s protocol. A) Example of over-fragmented sample that is outside the recommended range of 100-200bp (9 min of fragmentation). B) Optimal fragmentation result (~3 min). C) Under fragmented sample (1 min with higher concentration); although minimal under-fragmenation will likely still yield acceptable libraries, more extreme scenarios such as the one depicted will result in large amplicons that are outside the recommended range of the sequencer. “Lower” refers to the lower size marker for the TapeStation instrument.

    Journal: bioRxiv

    Article Title: Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline

    doi: 10.1101/2020.03.11.986174

    Figure Lengend Snippet: Agilent TapeStation 4200 results of RNA fragementation using High Sensitivity RNA ScreenTape. A small aliquot of total RNA (2μg) was fragemented for various durations at 70C and then a highly-diluted sample (~3ng/μL) was analyzed according to the manufacturer’s protocol. A) Example of over-fragmented sample that is outside the recommended range of 100-200bp (9 min of fragmentation). B) Optimal fragmentation result (~3 min). C) Under fragmented sample (1 min with higher concentration); although minimal under-fragmenation will likely still yield acceptable libraries, more extreme scenarios such as the one depicted will result in large amplicons that are outside the recommended range of the sequencer. “Lower” refers to the lower size marker for the TapeStation instrument.

    Article Snippet: While too little fragmentation results in amplicons that are outside the recommendations for Illumina sequencing (200-500bp for NovaSEQ 6000), over-fragmenting can result in a severe reduction in yield of appropriately sized immunoprecipitated RNA for input into the library preparation steps.

    Techniques: Concentration Assay, Marker

    Genus composition in Illumina ITS1 amplicon libraries constructed from DNA of fungal stained wood surfaces. ‘Unidentified’: sequences resulting in best hits with an identity below 97% or a query coverage below 90%

    Journal: Fungal Biology and Biotechnology

    Article Title: The fungal composition of natural biofinishes on oil-treated wood

    doi: 10.1186/s40694-017-0030-5

    Figure Lengend Snippet: Genus composition in Illumina ITS1 amplicon libraries constructed from DNA of fungal stained wood surfaces. ‘Unidentified’: sequences resulting in best hits with an identity below 97% or a query coverage below 90%

    Article Snippet: Mathematical analysis A Shannon’s diversity test was used to index the genus diversity in the Illumina amplicon data.

    Techniques: Amplification, Construct, Staining

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

    Journal: Microbes and Environments

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

    doi: 10.1264/jsme2.ME17188

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

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

    Techniques: Amplification, Sequencing, Construct

    Numerical comparison of terminal restriction fragment length polymorphism (T‐ RFLP ) analysis and Illumina 16S rRNA gene amplicon sequencing. (A) Number of terminal restriction fragments (TRFs) and operational taxonomic units (OTUs) obtained. TRF s are plotted in blue on the left y ‐axis and OTU s are plotted in red‐orange on the right. (B) Diversity indices of bacterial communities recovered by evaluated DNA extraction kits. Circle symbols show Shannon diversity and bars show Pielou's evenness. Diversity indices of fecal samples are plotted in shades of blue and ileal digesta samples in shades of red.

    Journal: MicrobiologyOpen

    Article Title: Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions

    doi: 10.1002/mbo3.312

    Figure Lengend Snippet: Numerical comparison of terminal restriction fragment length polymorphism (T‐ RFLP ) analysis and Illumina 16S rRNA gene amplicon sequencing. (A) Number of terminal restriction fragments (TRFs) and operational taxonomic units (OTUs) obtained. TRF s are plotted in blue on the left y ‐axis and OTU s are plotted in red‐orange on the right. (B) Diversity indices of bacterial communities recovered by evaluated DNA extraction kits. Circle symbols show Shannon diversity and bars show Pielou's evenness. Diversity indices of fecal samples are plotted in shades of blue and ileal digesta samples in shades of red.

    Article Snippet: Bacterial community profiles were analyzed with terminal restriction fragment length polymorphism (T‐RFLP) and bacterial community composition by Illumina amplicon sequencing spanning the V1–2 and V5–6 regions of the 16S rRNA gene.

    Techniques: Terminal Restriction Fragment Length Polymorphism, Amplification, Sequencing, DNA Extraction

    Nonmetric multidimensional scaling ( MDS ) plot comparing the global bacterial community of all samples analyzed with terminal restriction fragment length polymorphism (T‐ RFLP ) and Illumina amplicon sequencing. Abundance data were standardized with Bray–Curtis similarity algorithm. Symbols refer to cell lysis and DNA capture technique of the DNA extraction protocol.

    Journal: MicrobiologyOpen

    Article Title: Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions

    doi: 10.1002/mbo3.312

    Figure Lengend Snippet: Nonmetric multidimensional scaling ( MDS ) plot comparing the global bacterial community of all samples analyzed with terminal restriction fragment length polymorphism (T‐ RFLP ) and Illumina amplicon sequencing. Abundance data were standardized with Bray–Curtis similarity algorithm. Symbols refer to cell lysis and DNA capture technique of the DNA extraction protocol.

    Article Snippet: Bacterial community profiles were analyzed with terminal restriction fragment length polymorphism (T‐RFLP) and bacterial community composition by Illumina amplicon sequencing spanning the V1–2 and V5–6 regions of the 16S rRNA gene.

    Techniques: Terminal Restriction Fragment Length Polymorphism, Amplification, Sequencing, Lysis, DNA Extraction

    Cohort and sample processing outline. Thirty subject stool samples were collected from healthy subjects and adenoma (precancer) and carcinoma (cancer) patients. Stool samples were split into two aliquots, the first of which was used for bacterial sequencing and the second of which was used for virus sequencing. Bacterial sequencing was done using both 16S rRNA amplicon and whole-metagenomic shotgun sequencing techniques. Virus samples were purified for viruses using filtration and a combination of chloroform (bacterial lysis) and DNase (exposed genomic DNA degradation). The resulting encapsulated virus DNA was sequenced using whole-metagenomic shotgun sequencing.

    Journal: mBio

    Article Title: Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

    doi: 10.1128/mBio.02248-18

    Figure Lengend Snippet: Cohort and sample processing outline. Thirty subject stool samples were collected from healthy subjects and adenoma (precancer) and carcinoma (cancer) patients. Stool samples were split into two aliquots, the first of which was used for bacterial sequencing and the second of which was used for virus sequencing. Bacterial sequencing was done using both 16S rRNA amplicon and whole-metagenomic shotgun sequencing techniques. Virus samples were purified for viruses using filtration and a combination of chloroform (bacterial lysis) and DNase (exposed genomic DNA degradation). The resulting encapsulated virus DNA was sequenced using whole-metagenomic shotgun sequencing.

    Article Snippet: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform .

    Techniques: Sequencing, Amplification, Shotgun Sequencing, Purification, Filtration, Lysis

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-015-2194-9

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

    Article Snippet: We compared the fusion primer (FG) and tailed tag (t-tag) methodologies (Fig. ) for building amplicon libraries using the Illumina MiSeq platform.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Multiplexing

    Genome browser shot (hg19) illustrating the HAM-TBS FKBP5 panel and important locus-specific data. CTCF -ChIA-PET : track indicating the locations of CTCF ]). CTCF ChIP-seq and GR Chip-seq : regions of transcription factor binding derived from chromatin immunoprecipitation (ChIP) experiments in multiple cell lines from the ENCODE project; HAM-TBS FKBP5 panel : locations of the amplicons contained in this panel

    Journal: Epigenetics & Chromatin

    Article Title: HAM-TBS: high-accuracy methylation measurements via targeted bisulfite sequencing

    doi: 10.1186/s13072-018-0209-x

    Figure Lengend Snippet: Genome browser shot (hg19) illustrating the HAM-TBS FKBP5 panel and important locus-specific data. CTCF -ChIA-PET : track indicating the locations of CTCF ]). CTCF ChIP-seq and GR Chip-seq : regions of transcription factor binding derived from chromatin immunoprecipitation (ChIP) experiments in multiple cell lines from the ENCODE project; HAM-TBS FKBP5 panel : locations of the amplicons contained in this panel

    Article Snippet: The amplicons of all PCR reactions were quantified using the Agilent 2200 TapeStation (Agilent Technologies, Waldbronn, Germany] and equimolar pooled with the Hamilton pipetting robot.

    Techniques: ChIA Pet Assay, Chromatin Immunoprecipitation, Binding Assay, Derivative Assay

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

    Journal: Scientific Reports

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

    doi: 10.1038/s41598-018-35010-5

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

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

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

    Imprinted chromatin as a model system to quantify epigenetic influences on genome editing. (A) Schematic outlining the experimental workflow. Throughout the text, F1 hybrid cell lines are depicted with the maternal strain denoted before the paternal strain (i.e., In B×J: B is maternal and J paternal). sgRNAs are designed to cleave approximately 40–100 bp from a heterozygous SNP within imprinted chromatin (open and closed circles). MiSeq amplicons span both the SNP and site of mutation, which allows simultaneous assessment of genome editing outcome and parental allele at high-throughput. (B) Top: schematic showing the imprinted mouse Kcnq1 gene including H3K9me3 ChIP and DNase-I–seq data from mESCs available through EncODE (ENCSR000CFZ, GSM1014187) (bottom). Higher-resolution view of the KvDMR imprinted CpG island within Kcnq1 , showing the position of three sgRNAs used in panel E. (C) Allele-specific enrichment of H3K9me3 and H4K20me3. PCR fragments spanning the target sites of sgKvDMR#2 and #3 were amplified from input, or ChIP DNA prior to Sanger sequencing across an allelic SNP. gDNA = genomic DNA from purebred mice. (D) Example of CpG methylation data from the KvDMR . ChIP, chromatin immunoprecipitation; gDNA, genomic DNA; HDR, homology-directed repair; mESC, mouse embryonic stem cell, NHEJ, nonhomologous end joining; sgRNA, single guide RNA; SNP, single nucleotide polymorphism; SRA, Sequence Read Archive; ssODN, single-stranded oligodeoxynucleotide.

    Journal: PLoS Biology

    Article Title: Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

    doi: 10.1371/journal.pbio.2005595

    Figure Lengend Snippet: Imprinted chromatin as a model system to quantify epigenetic influences on genome editing. (A) Schematic outlining the experimental workflow. Throughout the text, F1 hybrid cell lines are depicted with the maternal strain denoted before the paternal strain (i.e., In B×J: B is maternal and J paternal). sgRNAs are designed to cleave approximately 40–100 bp from a heterozygous SNP within imprinted chromatin (open and closed circles). MiSeq amplicons span both the SNP and site of mutation, which allows simultaneous assessment of genome editing outcome and parental allele at high-throughput. (B) Top: schematic showing the imprinted mouse Kcnq1 gene including H3K9me3 ChIP and DNase-I–seq data from mESCs available through EncODE (ENCSR000CFZ, GSM1014187) (bottom). Higher-resolution view of the KvDMR imprinted CpG island within Kcnq1 , showing the position of three sgRNAs used in panel E. (C) Allele-specific enrichment of H3K9me3 and H4K20me3. PCR fragments spanning the target sites of sgKvDMR#2 and #3 were amplified from input, or ChIP DNA prior to Sanger sequencing across an allelic SNP. gDNA = genomic DNA from purebred mice. (D) Example of CpG methylation data from the KvDMR . ChIP, chromatin immunoprecipitation; gDNA, genomic DNA; HDR, homology-directed repair; mESC, mouse embryonic stem cell, NHEJ, nonhomologous end joining; sgRNA, single guide RNA; SNP, single nucleotide polymorphism; SRA, Sequence Read Archive; ssODN, single-stranded oligodeoxynucleotide.

    Article Snippet: Editing was quantified by Illumina sequencing of PCR amplicons spanning both the site of cleavage and an allelic SNP ( and , for detailed experimental protocols see ).

    Techniques: Mutagenesis, High Throughput Screening Assay, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Amplification, Sequencing, Mouse Assay, CpG Methylation Assay, Non-Homologous End Joining

    qChIP analysis of Cib1 binding to the pit1/2 - and tin1-1 -promoter. (A) Schematic overview of promoter organization and probe regions used for qChIP experiments. Sequence of the predicted Cib1 binding sites (UPRE) in the pit1/2 and tin1-1 promoter region is given in bold in case of identical nucleotides in pit1/2 and tin1-1 UPREs. (B) qChIP analysis of Cib1 binding to the pit1/2 and tin1-1 promoter in strain SG200 cib1-3xHA 3 h after DTT (3 mM) treatment. The HA-tagged Cib1 protein was immunoprecipitated with anti HA-antibody coupled agarose beads (Sigma). Enrichment of immunoprecipitated DNA is shown relative to the input control. PCR-amplicons corresponding to the pit1/2 and tin1-1 promoter are significantly enriched compared to ORF controls. No significant enrichment was observed for PCR-amplicons corresponding to pit1 , pit2 and tin1-1 ORFs in comparison to the eIF2b control. Given are the mean values of four independent experiments. Error bars represent the standard error (SE). Statistical significance was tested using Student's t -test. *indicates p-value

    Journal: PLoS ONE

    Article Title: Unfolded Protein Response (UPR) Regulator Cib1 Controls Expression of Genes Encoding Secreted Virulence Factors in Ustilago maydis

    doi: 10.1371/journal.pone.0153861

    Figure Lengend Snippet: qChIP analysis of Cib1 binding to the pit1/2 - and tin1-1 -promoter. (A) Schematic overview of promoter organization and probe regions used for qChIP experiments. Sequence of the predicted Cib1 binding sites (UPRE) in the pit1/2 and tin1-1 promoter region is given in bold in case of identical nucleotides in pit1/2 and tin1-1 UPREs. (B) qChIP analysis of Cib1 binding to the pit1/2 and tin1-1 promoter in strain SG200 cib1-3xHA 3 h after DTT (3 mM) treatment. The HA-tagged Cib1 protein was immunoprecipitated with anti HA-antibody coupled agarose beads (Sigma). Enrichment of immunoprecipitated DNA is shown relative to the input control. PCR-amplicons corresponding to the pit1/2 and tin1-1 promoter are significantly enriched compared to ORF controls. No significant enrichment was observed for PCR-amplicons corresponding to pit1 , pit2 and tin1-1 ORFs in comparison to the eIF2b control. Given are the mean values of four independent experiments. Error bars represent the standard error (SE). Statistical significance was tested using Student's t -test. *indicates p-value

    Article Snippet: Amplicons were normalized to the input control using the BioRad CFX manager software.

    Techniques: Binding Assay, Sequencing, Immunoprecipitation, Polymerase Chain Reaction

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

    Journal: Scientific Reports

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

    doi: 10.1038/srep13745

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

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

    Techniques: Mutagenesis, Clone Assay

    Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.

    Journal: PLoS ONE

    Article Title: Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells

    doi: 10.1371/journal.pone.0077443

    Figure Lengend Snippet: Neighbor-joining tree based on 16S rRNA gene sequences showing phylogenetic relationships in the genus Geobacter . Refer to Table 2 for the major OTUs. Desulfuromonas acetoxidans was used as an outgroup. Bootstrap values (100 trials, only > 50 are shown) are indicated at branching points. The bar indicates 2% sequence divergence. Accession numbers are shown in parentheses.

    Article Snippet: The microbiomes established in each system were compared by pyrotag sequencing of 16S rRNA gene amplicons and shotgun metagenomics.

    Techniques: Sequencing

    C57BL/6- Prnp ZH3/ZH3 mice do not have TALEN off-target cleavage sites. T7 endonuclease I digestion of PCR products generated from predicted OTs ( Table S1 ) and Prnp as a digestion positive control. Analyses were performed on the founder Prnp WT/ZH3 mouse and one control C57BL/6J mouse. Before enzymatic digestion, amplicons were subjected to a temperature gradient enabling the formation of heteroduplexes in the presence of heterozygous mutations in the amplified gDNA. In the presence of TALEN-induced mutations, fragments of the size indicated below the gels are expected to appear, in addition to the undigested, WT amplicon. Nonconsecutive lanes from the same gel show Prnp amplicon as a control. Only in the founder Prnp WT/ZH3 mouse T7 endonuclease I digestion of the Prnp amplicon results in the formation of the two predicted fragments (indicated by an asterisk).

    Journal: The Journal of Experimental Medicine

    Article Title: Strictly co-isogenic C57BL/6J-Prnp−/− mice: A rigorous resource for prion science

    doi: 10.1084/jem.20151610

    Figure Lengend Snippet: C57BL/6- Prnp ZH3/ZH3 mice do not have TALEN off-target cleavage sites. T7 endonuclease I digestion of PCR products generated from predicted OTs ( Table S1 ) and Prnp as a digestion positive control. Analyses were performed on the founder Prnp WT/ZH3 mouse and one control C57BL/6J mouse. Before enzymatic digestion, amplicons were subjected to a temperature gradient enabling the formation of heteroduplexes in the presence of heterozygous mutations in the amplified gDNA. In the presence of TALEN-induced mutations, fragments of the size indicated below the gels are expected to appear, in addition to the undigested, WT amplicon. Nonconsecutive lanes from the same gel show Prnp amplicon as a control. Only in the founder Prnp WT/ZH3 mouse T7 endonuclease I digestion of the Prnp amplicon results in the formation of the two predicted fragments (indicated by an asterisk).

    Article Snippet: Amplicons were subjected to agarose gel electrophoresis and DNA was purified from excised bands using the Nucleospin Gel and PCR Cleanup kit (Macherey-Nagel), according to manufacturer’s instructions.

    Techniques: Mouse Assay, Polymerase Chain Reaction, Generated, Positive Control, Amplification

    Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Journal: Virology Journal

    Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics

    doi: 10.1186/s12985-016-0504-8

    Figure Lengend Snippet: Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Article Snippet: Direct sequencing was attempted from amplicons cleaned using QIAquick columns or incubation at 65 °C for 15 min followed by centrifugation at 3800 rcf for 20 s. Amplicons were sent to Eurofins Genomics (Huntsville, AL) for sequencing using primer pair TYL828F/TYL834R.

    Techniques: Recombinase Polymerase Amplification, Generated, Infection, Polymerase Chain Reaction, Purification, Amplification, Staining

    PCR-single-strand conformational polymorphism of the ovine IGF-1 gene. Amplicons were electrophoresed on a 12% non-denaturing acrylamide/bis-acrylamide gel; 200 V, 4 °C for 12 h. Three SSCP patterns, GG, AA and GA were detected.

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: New polymorphism in the 5′ flanking region of IGF-1 gene and its association with wool traits in Egyptian Barki sheep

    doi: 10.1016/j.jgeb.2017.08.001

    Figure Lengend Snippet: PCR-single-strand conformational polymorphism of the ovine IGF-1 gene. Amplicons were electrophoresed on a 12% non-denaturing acrylamide/bis-acrylamide gel; 200 V, 4 °C for 12 h. Three SSCP patterns, GG, AA and GA were detected.

    Article Snippet: PCR amplicons were electrophoresed in 2% agarose gels, using 0.5X TBE buffer (89 mM Tris, 89 mM boric acid and 2 mM Na2 EDTA) containing 200 ng/ml of ethidium bromide and was visualized under UV light and photographed by Bio-Rad Laboratories, Hercules, CA, USA.

    Techniques: Polymerase Chain Reaction, Acrylamide Gel Assay

    Oncoprint visualizing the gene mutation status of APC , KRAS , NRAS , BRAF , PIK3CA , TP53 , FBXW7 and SMAD4 assessed by TruSeq Amplicon Cancer Panel TSACP analysis for stage II ( n = 29) and stage III ( n = 31) colon cancers The rows indicate the gene mutation status of the 60 samples (grey bars) and the black spots depict mutations.

    Journal: Oncotarget

    Article Title: Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients

    doi: 10.18632/oncotarget.12510

    Figure Lengend Snippet: Oncoprint visualizing the gene mutation status of APC , KRAS , NRAS , BRAF , PIK3CA , TP53 , FBXW7 and SMAD4 assessed by TruSeq Amplicon Cancer Panel TSACP analysis for stage II ( n = 29) and stage III ( n = 31) colon cancers The rows indicate the gene mutation status of the 60 samples (grey bars) and the black spots depict mutations.

    Article Snippet: Detection of gene mutations Mutation status of APC , TP53 , KRAS , PIK3CA , FBXW7 , SMAD4 , BRAF and NRAS , i.e. genes that are commonly mutated in CRC, was assessed by next generation sequencing analysis of FFPE DNA samples using the TruSeq Amplicon Cancer Panel (TSACP; Illumina Inc, San Diego, CA USA).

    Techniques: Mutagenesis, Amplification

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

    Journal: Frontiers in Immunology

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

    doi: 10.3389/fimmu.2017.01796

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

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

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

    Generation and characterization of MISTR1 KO A549 cells. A) CRISPR/CAS deletion strategy for MISTR1 . Scissors indicate relative locations of guide RNAs designed to target sequences flanking exon 2 of this gene. The exon 2 deletion strategy was employed for ease of genotyping. Gene structure from UCSC genome browser. Sequences of breakpoints identified a 225bp deletion that included exon 2. Note identical repaired breakpoints were recovered for both clones. B) Agarose gel resolving amplicons from genotyping PCR of A549 KO clones. C) Western blot analysis using lysates from WT and MISTR1 KO clones. D) Measurement of proliferation rates using IncuCyte for MISTR1 KO A549 cell line. Changes in % confluence were used as a surrogate marker of cell proliferation. Data represent means ± SD (n=6 replicates). E) Western blot analysis of cleaved PARP levels using lysates from WT and MISTR1 KO cells following 16 hours of STS treatment. Densitometry analysis of PARP levels was performed using Image Lab version 6.0.1 (Bio-Rad). % Cleaved PARP= (cleaved PARP/(Full + Cleaved PARP)) * 100. STS - staurosporine.

    Journal: bioRxiv

    Article Title: MISTR: A conserved MItochondrial STress Response network revealed by signatures of evolutionary conflict

    doi: 10.1101/2020.01.25.919811

    Figure Lengend Snippet: Generation and characterization of MISTR1 KO A549 cells. A) CRISPR/CAS deletion strategy for MISTR1 . Scissors indicate relative locations of guide RNAs designed to target sequences flanking exon 2 of this gene. The exon 2 deletion strategy was employed for ease of genotyping. Gene structure from UCSC genome browser. Sequences of breakpoints identified a 225bp deletion that included exon 2. Note identical repaired breakpoints were recovered for both clones. B) Agarose gel resolving amplicons from genotyping PCR of A549 KO clones. C) Western blot analysis using lysates from WT and MISTR1 KO clones. D) Measurement of proliferation rates using IncuCyte for MISTR1 KO A549 cell line. Changes in % confluence were used as a surrogate marker of cell proliferation. Data represent means ± SD (n=6 replicates). E) Western blot analysis of cleaved PARP levels using lysates from WT and MISTR1 KO cells following 16 hours of STS treatment. Densitometry analysis of PARP levels was performed using Image Lab version 6.0.1 (Bio-Rad). % Cleaved PARP= (cleaved PARP/(Full + Cleaved PARP)) * 100. STS - staurosporine.

    Article Snippet: Clones of interest were identified by PCR on genomic DNA harvested with the Quick -DNA Miniprep Kit (Zymo) from expanded cell lines using primers flanking exon 2 followed by Sanger sequencing of amplicons by Genewiz.

    Techniques: CRISPR, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Western Blot, Marker

    A. PCR amplicons generated from primer pair 11 in 9 plant species . Fa – Fragaria × ananassa /Rosaceae, Pp – Prunus persica /Rosaceae, At – Arabidopsis thaliana /Crucifereae, Cs – Citrus sinensis /Rutaceae, Ch – Coleus hybrida /Lamiaceae, Nt – Nicotiana tabacum /Solanaceae, Le – Lycopersicon esculentum /Solanaceae, Ls – Lactuca sativa /Asteraceae, Ah – Amaranthus hypochondriacus /Caryophyllaceae. B . Schematic representation of the polymorphism between the amplicons generated from primer pair 11 in tobacco, tomato and amaranthus.

    Journal: BMC Genomics

    Article Title: ASAP: Amplification, sequencing annotation of plastomes

    doi: 10.1186/1471-2164-6-176

    Figure Lengend Snippet: A. PCR amplicons generated from primer pair 11 in 9 plant species . Fa – Fragaria × ananassa /Rosaceae, Pp – Prunus persica /Rosaceae, At – Arabidopsis thaliana /Crucifereae, Cs – Citrus sinensis /Rutaceae, Ch – Coleus hybrida /Lamiaceae, Nt – Nicotiana tabacum /Solanaceae, Le – Lycopersicon esculentum /Solanaceae, Ls – Lactuca sativa /Asteraceae, Ah – Amaranthus hypochondriacus /Caryophyllaceae. B . Schematic representation of the polymorphism between the amplicons generated from primer pair 11 in tobacco, tomato and amaranthus.

    Article Snippet: These amplicons were generated using Pfu Turbo DNA polymerase (Stratagene Inc., Carlsbad, CA) in order to minimize potential errors generated during PCR reactions.

    Techniques: Polymerase Chain Reaction, Generated

    Composite ASAP PCR profiles from 8 plant species . At – Arabidopsis thaliana , Nt – Nicotiana tabacum , Cs – Citrus sinensis , Pp – Prunus persica , Le – Lycopersicon esculentum , Ah – Amaranthus hypochondriacus , Ch – Coleus hybrida and Ls – Lactuca sativa . Horizontal lines across each species indicate 1 kb size. Vertical columns indicate the amplicons generated from a given primer pair in the 8 plant species.

    Journal: BMC Genomics

    Article Title: ASAP: Amplification, sequencing annotation of plastomes

    doi: 10.1186/1471-2164-6-176

    Figure Lengend Snippet: Composite ASAP PCR profiles from 8 plant species . At – Arabidopsis thaliana , Nt – Nicotiana tabacum , Cs – Citrus sinensis , Pp – Prunus persica , Le – Lycopersicon esculentum , Ah – Amaranthus hypochondriacus , Ch – Coleus hybrida and Ls – Lactuca sativa . Horizontal lines across each species indicate 1 kb size. Vertical columns indicate the amplicons generated from a given primer pair in the 8 plant species.

    Article Snippet: These amplicons were generated using Pfu Turbo DNA polymerase (Stratagene Inc., Carlsbad, CA) in order to minimize potential errors generated during PCR reactions.

    Techniques: Polymerase Chain Reaction, Generated

    Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the 16S rRNA V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Prevalence of Mycoplasma lineages in Senegalese rodents, by site, and phylogenetic associations between Mycoplasma lineages and rodent species. (A) Comparison of phylogenetic trees based on the 16S rRNA V4 sequences of Mycoplasma and on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR) for rodents (the tree was drawn based on data from reference 92 ). Lines link the Mycoplasma lineages detected in the various rodent species (for a minimum site prevalence exceeding 10%). The numbers next to the branches are bootstrap values (shown only if > 70%). (B) Plots of OTU prevalences, with 95% confidence intervals calculated by Sterne’s exact method ( 93 ) according to rodent species and site (see reference 69 for more information about site codes and their geographic locations). The gray bars on the x axis indicate sites from which the rodent species concerned is absent.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques:

    Taxonomic assignment of the V4 16S rRNA sequences in wild rodents and in negative controls for extraction and PCR. The histograms show the percentages of sequences for the most abundant bacterial genera in the two MiSeq runs combined. Notice the presence in the controls of several bacterial genera, which was likely due to the inherent contamination of laboratory reagents by bacterial DNA (termed “contaminant genera”). These contaminant genera are also present (to a lesser extent) in the rodent samples. The insertions represent the proportion of sequences from rodent samples which were incorrectly assigned to the controls. See Fig. S1 for separate histograms for the two MiSeq runs.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Taxonomic assignment of the V4 16S rRNA sequences in wild rodents and in negative controls for extraction and PCR. The histograms show the percentages of sequences for the most abundant bacterial genera in the two MiSeq runs combined. Notice the presence in the controls of several bacterial genera, which was likely due to the inherent contamination of laboratory reagents by bacterial DNA (termed “contaminant genera”). These contaminant genera are also present (to a lesser extent) in the rodent samples. The insertions represent the proportion of sequences from rodent samples which were incorrectly assigned to the controls. See Fig. S1 for separate histograms for the two MiSeq runs.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques: Polymerase Chain Reaction

    Workflow of the wet laboratory, bioinformatics, and data filtering procedures in the process of data filtering for 16S rRNA amplicon sequencing. Reagent contaminants were detected by analyzing the sequences in the NC ext and NC PCR controls. Sequence number thresholds for correcting for cross-contamination (T CC ) are OTU and run dependent and were estimated by analyzing the sequences in the NC mus , NC ext , NC PCR , and PC index controls. Sequence number thresholds for correcting for false-index-pairing (T FA ) values are OTU and run dependent and were estimated by analyzing the sequences in the NC index and PC alien controls. A result was considered positive if the number of sequences was > T CC and > T FA . Samples were considered positive if a positive result was obtained for both PCR replicates. *, see Kozich et al. ( 18 ) for details on the sequencing.

    Journal: mSystems

    Article Title: 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

    doi: 10.1128/mSystems.00032-16

    Figure Lengend Snippet: Workflow of the wet laboratory, bioinformatics, and data filtering procedures in the process of data filtering for 16S rRNA amplicon sequencing. Reagent contaminants were detected by analyzing the sequences in the NC ext and NC PCR controls. Sequence number thresholds for correcting for cross-contamination (T CC ) are OTU and run dependent and were estimated by analyzing the sequences in the NC mus , NC ext , NC PCR , and PC index controls. Sequence number thresholds for correcting for false-index-pairing (T FA ) values are OTU and run dependent and were estimated by analyzing the sequences in the NC index and PC alien controls. A result was considered positive if the number of sequences was > T CC and > T FA . Samples were considered positive if a positive result was obtained for both PCR replicates. *, see Kozich et al. ( 18 ) for details on the sequencing.

    Article Snippet: Such HTS microbial identification approaches are based on the sequencing of all (WGS [whole-genome sequencing]) or some (RNA-seq [whole-RNA sequencing] or 16S rRNA amplicon sequencing) of the bacterial DNA or RNA in a sample, followed by comparison to a reference sequence database ( ).

    Techniques: Amplification, Sequencing, Polymerase Chain Reaction

    Silencing of KLK6 expression in FaDu cells promotes tumor cell proliferation. ( A ) KLK6 expression in human HNSCC (FaDu, Cal27, SCC25) and HeLa cervix carcinoma cells was monitored on protein level by Western blot analysis with cell culture supernatants (upper panel), and on transcript level by semi-quantitative (middle panels) as well as quantitative RT-PCR (lower graph). Detection of LMNB1 amplicons served as control for cDNA quality and quantity for semi-quantitative RT-PCR (lower panel), while transcript levels of three independent reference genes ( ACTB, LMNB1, TBP ) were used for quantitative RT-PCR data. ( B ) KLK6 expression in stable FaDu-Mock and FaDu-shKLK6 clones is given by semi-quantitative (upper panel) and quantitative RT-PCR (lower graph) and was determined as described in ( A ). Differences in tumor cell proliferation between stable FaDu-Mock and FaDu-shKLK6 clones was monitored by quantification of cell counts over a time period of six days ( C ) and a BrdU incorporation assay ( D ). The graph represents mean values and standard deviations (SD) of the percentage total of BrdU-positive cells from three independent FaDu-shKLK6 clones and mock controls, respectively

    Journal: Molecular Cancer

    Article Title: Kallikrein-related peptidase 6 regulates epithelial-to-mesenchymal transition and serves as prognostic biomarker for head and neck squamous cell carcinoma patients

    doi: 10.1186/s12943-015-0381-6

    Figure Lengend Snippet: Silencing of KLK6 expression in FaDu cells promotes tumor cell proliferation. ( A ) KLK6 expression in human HNSCC (FaDu, Cal27, SCC25) and HeLa cervix carcinoma cells was monitored on protein level by Western blot analysis with cell culture supernatants (upper panel), and on transcript level by semi-quantitative (middle panels) as well as quantitative RT-PCR (lower graph). Detection of LMNB1 amplicons served as control for cDNA quality and quantity for semi-quantitative RT-PCR (lower panel), while transcript levels of three independent reference genes ( ACTB, LMNB1, TBP ) were used for quantitative RT-PCR data. ( B ) KLK6 expression in stable FaDu-Mock and FaDu-shKLK6 clones is given by semi-quantitative (upper panel) and quantitative RT-PCR (lower graph) and was determined as described in ( A ). Differences in tumor cell proliferation between stable FaDu-Mock and FaDu-shKLK6 clones was monitored by quantification of cell counts over a time period of six days ( C ) and a BrdU incorporation assay ( D ). The graph represents mean values and standard deviations (SD) of the percentage total of BrdU-positive cells from three independent FaDu-shKLK6 clones and mock controls, respectively

    Article Snippet: Amplicons were separated by 1 % agarose gel electrophoresis and visualized with GelRed (Biotium, USA) using the UV documentation system for agarose gel (peqlab, Germany).

    Techniques: Expressing, Western Blot, Cell Culture, Quantitative RT-PCR, Clone Assay, BrdU Incorporation Assay

    Maximum-likelihood tree of 16S rRNA gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.

    Journal: Frontiers in Microbiology

    Article Title: “Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

    doi: 10.3389/fmicb.2018.03159

    Figure Lengend Snippet: Maximum-likelihood tree of 16S rRNA gene sequences derived from the metagenome bins analyzed in this study and closely related partial genomes showing their phylogenetic affiliation with the “ Chlorobi lineage 5” (OPB56 clade, “ Ca. Kapabacteria”). Percentage numbers on nodes refer to 100 bootstrap pseudo-replicates conducted. Only values > 50% are shown. Scale bar represents 0.1 changes per nucleotide position.

    Article Snippet: Metagenome and 16S rRNA gene amplicon sequencing was conducted on Illumina HiSeq and MiSeq instruments, respectively, as described previously ( , ).

    Techniques: Derivative Assay

    Maximum likelihood tree with 200 bootstrap replicates for Papilio 5’ invected . Papilio dardanus individuals are represented by haplotypes from MiSeq amplicon sequencing. Note that P. demodocus and P. memnon are paraphyletic. Blue dots indicate nodes with bootstrap support > 70%. Bootstrap support at intraspecific nodes is not presented.

    Journal: BMC Evolutionary Biology

    Article Title: The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus

    doi: 10.1186/1471-2148-14-140

    Figure Lengend Snippet: Maximum likelihood tree with 200 bootstrap replicates for Papilio 5’ invected . Papilio dardanus individuals are represented by haplotypes from MiSeq amplicon sequencing. Note that P. demodocus and P. memnon are paraphyletic. Blue dots indicate nodes with bootstrap support > 70%. Bootstrap support at intraspecific nodes is not presented.

    Article Snippet: Additional file 1: Table S1: Table of samples of Papilio used for phylogenetic analysis of engrailed and invected. (XLSX 41 KB) Additional file 2: Table S2: Table of PCR primers. (XLSX 8 KB) Additional file 3: Table S3: Table of samples used for Illumina MiSeq amplicon sequencing to infer haplotypes. (XLSX 9 KB) Additional file 4: Table S4: Table of samples of P. dardanus used for phylogenetic and haplotype-level analysis. (XLSX 13 KB) Additional file 5: Table S5: Table of samples of P. dardanus cenea from Mpaphuli Cycad Reserve population used in population genetic analyses. (XLSX 17 KB) Additional file 6: Figure S1: Maximum likelihood phylogeny of cytohrome b amplicon within the P. dardanus species group.

    Techniques: Amplification, Sequencing

    ML phylogeny of 5’ engrailed across the genus Papilio , with a Battus outgroup. Papilio dardanus individuals are represented by haplotypes from either cloning or MiSeq amplicon sequencing. Blue dots indicate nodes with bootstrap support > 70%. Bootstraps at intraspecific nodes are ignored.

    Journal: BMC Evolutionary Biology

    Article Title: The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus

    doi: 10.1186/1471-2148-14-140

    Figure Lengend Snippet: ML phylogeny of 5’ engrailed across the genus Papilio , with a Battus outgroup. Papilio dardanus individuals are represented by haplotypes from either cloning or MiSeq amplicon sequencing. Blue dots indicate nodes with bootstrap support > 70%. Bootstraps at intraspecific nodes are ignored.

    Article Snippet: Additional file 1: Table S1: Table of samples of Papilio used for phylogenetic analysis of engrailed and invected. (XLSX 41 KB) Additional file 2: Table S2: Table of PCR primers. (XLSX 8 KB) Additional file 3: Table S3: Table of samples used for Illumina MiSeq amplicon sequencing to infer haplotypes. (XLSX 9 KB) Additional file 4: Table S4: Table of samples of P. dardanus used for phylogenetic and haplotype-level analysis. (XLSX 13 KB) Additional file 5: Table S5: Table of samples of P. dardanus cenea from Mpaphuli Cycad Reserve population used in population genetic analyses. (XLSX 17 KB) Additional file 6: Figure S1: Maximum likelihood phylogeny of cytohrome b amplicon within the P. dardanus species group.

    Techniques: Clone Assay, Amplification, Sequencing