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    Thermo Fisher geneart seamless cloning
    Geneart Seamless Cloning, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1491 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa in fusion hd cloning kit
    Comparison of phenotypes and genotypes between parental ey Δ877/Δ1 strain and HR revertants. ( a ) Lateral pictures of wild type (left), parental ey Δ877/Δ1 strain (centre), and HR revertant (right). The ey Δ877/Δ1 strain shows the deformed, non-spherical compound eye (ce) phenotype. The HR revertant shows the normal eye phenotype and wild type strain. Scale bar indicates 100 μm. ( b ) Schematic illustration of genomic <t>PCR</t> to check the integration of attP into the Dma-ey Δ1 allele. Black thick bar indicates the Dma-ey Δ1 allele. Primers are shown by arrows. The attP knock-in results in 240 bp long PCR products, whereas no modification gives 173 bp long PCR products. ( c ) Agarose gel electrophoresis of genomic PCR products using HR revertant strains. 1 and 2 are derived from co-injection of <t>TALEN</t> mRNAs and targeting plasmid, whereas 3 is derived from co-injection of TALEN mRNAs and ssODN with 80 nt homology. attP knocked-in HR revertants showed 240 bp PCR products, whereas parental ey Δ877/Δ1 strain showed 173 bp PCR products. M indicates the marker DNA.
    In Fusion Hd Cloning Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 16768 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextera dna flex library prep kit
    Application of <t>Nextera</t> <t>DNA</t> Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum
    Nextera Dna Flex Library Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextera xt dna library preparation kit
    Application of <t>Nextera</t> <t>DNA</t> Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum
    Nextera Xt Dna Library Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 5345 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextera xt kit
    Application of <t>Nextera</t> <t>DNA</t> Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum
    Nextera Xt Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 4497 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq rna sample preparation kit v2
    Application of <t>Nextera</t> <t>DNA</t> Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum
    Truseq Rna Sample Preparation Kit V2, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 7098 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher alamarblue
    Restricted glycolysis enhances the SCLC cell population in breast cancer cells (A) Mammosphere assay. 8-10 days after plating in mammosphere culture conditions, representative images were captured by microscopy (bar 100 μm) and mammospheres were measured by <t>alamarBlue.</t> (one sample t -test). (B) ALDEFLUOR assay; diethylaminobenzaldehyde (DEAB), was used to establish the baseline fluorescence. Flow cytometry plots indicate side scatter (SSC) versus fluorescence intensity. (C) Flow cytometric assessment of surface CD24 and CD44 expression. (B, C) representative of one of three biological repeats. (D) Colony assay; 18 h after plating, media was replaced with media containing either DMSO carrier control or paclitaxel (5 nM) and cells allowed to grow for 8-10 days. (one way ANOVA and Fisher’s LSD test).
    Alamarblue, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3352 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher lipofectamine 2000
    Restricted glycolysis enhances the SCLC cell population in breast cancer cells (A) Mammosphere assay. 8-10 days after plating in mammosphere culture conditions, representative images were captured by microscopy (bar 100 μm) and mammospheres were measured by <t>alamarBlue.</t> (one sample t -test). (B) ALDEFLUOR assay; diethylaminobenzaldehyde (DEAB), was used to establish the baseline fluorescence. Flow cytometry plots indicate side scatter (SSC) versus fluorescence intensity. (C) Flow cytometric assessment of surface CD24 and CD44 expression. (B, C) representative of one of three biological repeats. (D) Colony assay; 18 h after plating, media was replaced with media containing either DMSO carrier control or paclitaxel (5 nM) and cells allowed to grow for 8-10 days. (one way ANOVA and Fisher’s LSD test).
    Lipofectamine 2000, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 466214 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher fluo 4
    Comparison of Ca i 2+ transients measured using high-affinity dye <t>Fluo-4</t> (site 1, green traces) and low-affinity dye Fluo-4FF (site 2, red traces), and corresponding V m recordings (blue traces) at different CLs ( A–D ). Green dashed lines duplicate
    Fluo 4, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7892 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc illumina adapter
    Comparison of Ca i 2+ transients measured using high-affinity dye <t>Fluo-4</t> (site 1, green traces) and low-affinity dye Fluo-4FF (site 2, red traces), and corresponding V m recordings (blue traces) at different CLs ( A–D ). Green dashed lines duplicate
    Illumina Adapter, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 356 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Comparison of phenotypes and genotypes between parental ey Δ877/Δ1 strain and HR revertants. ( a ) Lateral pictures of wild type (left), parental ey Δ877/Δ1 strain (centre), and HR revertant (right). The ey Δ877/Δ1 strain shows the deformed, non-spherical compound eye (ce) phenotype. The HR revertant shows the normal eye phenotype and wild type strain. Scale bar indicates 100 μm. ( b ) Schematic illustration of genomic PCR to check the integration of attP into the Dma-ey Δ1 allele. Black thick bar indicates the Dma-ey Δ1 allele. Primers are shown by arrows. The attP knock-in results in 240 bp long PCR products, whereas no modification gives 173 bp long PCR products. ( c ) Agarose gel electrophoresis of genomic PCR products using HR revertant strains. 1 and 2 are derived from co-injection of TALEN mRNAs and targeting plasmid, whereas 3 is derived from co-injection of TALEN mRNAs and ssODN with 80 nt homology. attP knocked-in HR revertants showed 240 bp PCR products, whereas parental ey Δ877/Δ1 strain showed 173 bp PCR products. M indicates the marker DNA.

    Journal: Scientific Reports

    Article Title: TALEN-mediated homologous recombination in Daphnia magna

    doi: 10.1038/srep18312

    Figure Lengend Snippet: Comparison of phenotypes and genotypes between parental ey Δ877/Δ1 strain and HR revertants. ( a ) Lateral pictures of wild type (left), parental ey Δ877/Δ1 strain (centre), and HR revertant (right). The ey Δ877/Δ1 strain shows the deformed, non-spherical compound eye (ce) phenotype. The HR revertant shows the normal eye phenotype and wild type strain. Scale bar indicates 100 μm. ( b ) Schematic illustration of genomic PCR to check the integration of attP into the Dma-ey Δ1 allele. Black thick bar indicates the Dma-ey Δ1 allele. Primers are shown by arrows. The attP knock-in results in 240 bp long PCR products, whereas no modification gives 173 bp long PCR products. ( c ) Agarose gel electrophoresis of genomic PCR products using HR revertant strains. 1 and 2 are derived from co-injection of TALEN mRNAs and targeting plasmid, whereas 3 is derived from co-injection of TALEN mRNAs and ssODN with 80 nt homology. attP knocked-in HR revertants showed 240 bp PCR products, whereas parental ey Δ877/Δ1 strain showed 173 bp PCR products. M indicates the marker DNA.

    Article Snippet: Finally, the attP fragments were cloned into the TALEN-targeted site of the pCR-BluntII-Dma-ey1.5kb by the In-Fusion PCR cloning kit (Clontech, California, USA).

    Techniques: Polymerase Chain Reaction, Knock-In, Modification, Agarose Gel Electrophoresis, Derivative Assay, Injection, Plasmid Preparation, Marker

    Establishment and use of Dma-lig4 deficient mutant by CRISPR/Cas. ( a ) Schematic gene structure of Dma-lig4 . Dma-lig4 gene is annotated to consist of 8 exons (open boxes). Putative catalytic domain-encoding regions are highlighted in yellow (adenylation domain) and light green (oligonucleotide binding fold domain). gRNA-targeted sites are shown by triangles. Primers used for RT-PCR are shown by black arrows. Scale bar indicates 0.2 kb. ( b ) PAGE analyses around gRNA #2 target site of putative Dma-lig4 mutants. The genomic region surrounding gRNA #2 target site was amplified from genome DNAs of randomly selected 18 G1 lines. The original size of the PCR products should be 145 bp, indicated by black arrows. Thus, different patterns of band migration indicate the various in-del formation on the gRNA #2 targeted site. Asterisks (*) show the putative monoallelic and/or biallelic mutants. M indicates the marker DNA. ( c ) Genotype of Dma-lig4 biallelic mutant strain. Deduced amino acid sequences of wild type or Dma-lig4 mutant #14 are shown under the genome DNA sequences. gRNA #2 targeted sequences and Protospacer Adjacent Motif (PAM) are lined. Especially, gRNA #2 targeted sequences are highlighted in bold. Lower case indicates the introduced in-del mutations into mutant #14 genome. As shown in red, a premature termination codon was introduced into both Dma-lig4 alleles in the mutant #14 genome. ( d , e ) PAGE analyses of G1 offspring from TALEN and targeting plasmid injection using ey Δ877/Δ1 strain with or without Dma-ey deficiency (d, e, respectively). To estimate the germ line in-del mutation rate, the genomic region surrounding the TALEN targeted site was amplified from genome DNAs of randomly selected 24 G1 lines. Original size of the PCR products should be 173 bp, indicated by black arrows. Thus, different patterns of band migration indicate the various in-del formations on TALEN targeted site. Asterisks (*) show the putative in-del introduced lines. M indicates the marker DNA.

    Journal: Scientific Reports

    Article Title: TALEN-mediated homologous recombination in Daphnia magna

    doi: 10.1038/srep18312

    Figure Lengend Snippet: Establishment and use of Dma-lig4 deficient mutant by CRISPR/Cas. ( a ) Schematic gene structure of Dma-lig4 . Dma-lig4 gene is annotated to consist of 8 exons (open boxes). Putative catalytic domain-encoding regions are highlighted in yellow (adenylation domain) and light green (oligonucleotide binding fold domain). gRNA-targeted sites are shown by triangles. Primers used for RT-PCR are shown by black arrows. Scale bar indicates 0.2 kb. ( b ) PAGE analyses around gRNA #2 target site of putative Dma-lig4 mutants. The genomic region surrounding gRNA #2 target site was amplified from genome DNAs of randomly selected 18 G1 lines. The original size of the PCR products should be 145 bp, indicated by black arrows. Thus, different patterns of band migration indicate the various in-del formation on the gRNA #2 targeted site. Asterisks (*) show the putative monoallelic and/or biallelic mutants. M indicates the marker DNA. ( c ) Genotype of Dma-lig4 biallelic mutant strain. Deduced amino acid sequences of wild type or Dma-lig4 mutant #14 are shown under the genome DNA sequences. gRNA #2 targeted sequences and Protospacer Adjacent Motif (PAM) are lined. Especially, gRNA #2 targeted sequences are highlighted in bold. Lower case indicates the introduced in-del mutations into mutant #14 genome. As shown in red, a premature termination codon was introduced into both Dma-lig4 alleles in the mutant #14 genome. ( d , e ) PAGE analyses of G1 offspring from TALEN and targeting plasmid injection using ey Δ877/Δ1 strain with or without Dma-ey deficiency (d, e, respectively). To estimate the germ line in-del mutation rate, the genomic region surrounding the TALEN targeted site was amplified from genome DNAs of randomly selected 24 G1 lines. Original size of the PCR products should be 173 bp, indicated by black arrows. Thus, different patterns of band migration indicate the various in-del formations on TALEN targeted site. Asterisks (*) show the putative in-del introduced lines. M indicates the marker DNA.

    Article Snippet: Finally, the attP fragments were cloned into the TALEN-targeted site of the pCR-BluntII-Dma-ey1.5kb by the In-Fusion PCR cloning kit (Clontech, California, USA).

    Techniques: Mutagenesis, CRISPR, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Amplification, Polymerase Chain Reaction, Migration, Marker, Plasmid Preparation, Injection

    Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Article Snippet: All reagents listed below are included in the Nextera DNA Flex kit (Illumina, cat. Nos.

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated

    Nextera DNA Flex Library Prep workflow overview. * Time estimates based on preparing 16 samples using a multichannel pipette. BLB, blood lysis buffer. BLT, bead-linked transposome. EPM, enhanced PCR mix. EtOH, Ethanol. PK1, proteinase K. RSB, resuspension buffer. SPB, sample purification beads. TB1, tagmentation buffer 1. TSB, tagment stop buffer. TWB, tagment wash buffer

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Nextera DNA Flex Library Prep workflow overview. * Time estimates based on preparing 16 samples using a multichannel pipette. BLB, blood lysis buffer. BLT, bead-linked transposome. EPM, enhanced PCR mix. EtOH, Ethanol. PK1, proteinase K. RSB, resuspension buffer. SPB, sample purification beads. TB1, tagmentation buffer 1. TSB, tagment stop buffer. TWB, tagment wash buffer

    Article Snippet: All reagents listed below are included in the Nextera DNA Flex kit (Illumina, cat. Nos.

    Techniques: Transferring, Lysis, Polymerase Chain Reaction, Purification

    Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Article Snippet: All reagents listed below are included in the Nextera DNA Flex kit (Illumina, cat. Nos.

    Techniques: Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction

    Improved coverage of human and bacterial genomes with Nextera DNA Flex. a Coverage across important regions of the human genome by three library preparation kits: Nextera DNA Flex, TruSeq Nano, and TruSeq PCR-free. b Coverage across extreme regions of the human genome by three library preparation kits: Nextera DNA Flex, TruSeq Nano, and TruSeq PCR-free. c Libraries generated from the small genomes of bacteria with low ( B. cereus ), medium ( E. coli ), and high ( R. sphaeroides ) GC content at 1 ng inputs. Less coverage variation was observed with libraries prepared by Nextera DNA Flex compared with libraries prepared by other commercially available library preparation kits (NEB, NEBNext Ultra DNA Library Prep Kit; Kapa A, Kapa HyperPlus Kits; Kapa B, Kapa HyperPrep Kits), particularly for the low and high GC content genomes of B. cereus and R. sphaeroides. The method of DNA fragmentation and whether PCR amplification was used during library preparation is indicated

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Improved coverage of human and bacterial genomes with Nextera DNA Flex. a Coverage across important regions of the human genome by three library preparation kits: Nextera DNA Flex, TruSeq Nano, and TruSeq PCR-free. b Coverage across extreme regions of the human genome by three library preparation kits: Nextera DNA Flex, TruSeq Nano, and TruSeq PCR-free. c Libraries generated from the small genomes of bacteria with low ( B. cereus ), medium ( E. coli ), and high ( R. sphaeroides ) GC content at 1 ng inputs. Less coverage variation was observed with libraries prepared by Nextera DNA Flex compared with libraries prepared by other commercially available library preparation kits (NEB, NEBNext Ultra DNA Library Prep Kit; Kapa A, Kapa HyperPlus Kits; Kapa B, Kapa HyperPrep Kits), particularly for the low and high GC content genomes of B. cereus and R. sphaeroides. The method of DNA fragmentation and whether PCR amplification was used during library preparation is indicated

    Article Snippet: All reagents listed below are included in the Nextera DNA Flex kit (Illumina, cat. Nos.

    Techniques: Polymerase Chain Reaction, Generated, Amplification

    Quality comparison of E. coli and S. aureus genome assemblies obtained by library preparation kits. (A) Assembly statistics obtained by six library preparation kits were compared in E. coli and S. aureus . Two E. coli and two S. aureus genomes were analysed as model bacterial genomes to compare six library preparation kits. Illumina read sequences obtained from each library were assembled using Velvet and SPAdes, and the numbers of contigs and L50 values of each assembly are shown. In each sequence data set, assembly was repeated 10 times using Illumina reads randomly selected at 30× coverage. Error bars indicate standard deviations. The six kits used cover three fragmentation strategies (see the main text). XT, Nextera XT; FL, Nextera DNA Flex; KP, KAPA HyperPlus; NN, NEBNext Ultra II; QS, QIAseq FX; and TS, TruSeq nano. (B) Relative sequence coverage in relation to GC content was calculated in E. coli and S. aureus genomes obtained by three library preparation kits. Relative sequence coverage in the genome assemblies obtained by the XT, FL, and KP kits and GC content were calculated for every 200-bp window with no overlap. Only the first 120,000 bp regions of each genome are shown. (C) Relationships between GC content and sequence coverage in the E. coli and S. aureus genome assemblies obtained by six library preparation kits are shown. The relative abundance of 200 bp bins with a given GC content (defined by 0.5% interval) and the mean relative coverage of bins with a given GC content ( C GC ) were calculated and are shown along with GC content by black lines or lines coloured according to the library preparation kits, respectively. Black horizontal lines ( C GC =1) represent unbiased coverage. The data for bins with extreme GC content (those representing

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes

    doi: 10.1093/dnares/dsz017

    Figure Lengend Snippet: Quality comparison of E. coli and S. aureus genome assemblies obtained by library preparation kits. (A) Assembly statistics obtained by six library preparation kits were compared in E. coli and S. aureus . Two E. coli and two S. aureus genomes were analysed as model bacterial genomes to compare six library preparation kits. Illumina read sequences obtained from each library were assembled using Velvet and SPAdes, and the numbers of contigs and L50 values of each assembly are shown. In each sequence data set, assembly was repeated 10 times using Illumina reads randomly selected at 30× coverage. Error bars indicate standard deviations. The six kits used cover three fragmentation strategies (see the main text). XT, Nextera XT; FL, Nextera DNA Flex; KP, KAPA HyperPlus; NN, NEBNext Ultra II; QS, QIAseq FX; and TS, TruSeq nano. (B) Relative sequence coverage in relation to GC content was calculated in E. coli and S. aureus genomes obtained by three library preparation kits. Relative sequence coverage in the genome assemblies obtained by the XT, FL, and KP kits and GC content were calculated for every 200-bp window with no overlap. Only the first 120,000 bp regions of each genome are shown. (C) Relationships between GC content and sequence coverage in the E. coli and S. aureus genome assemblies obtained by six library preparation kits are shown. The relative abundance of 200 bp bins with a given GC content (defined by 0.5% interval) and the mean relative coverage of bins with a given GC content ( C GC ) were calculated and are shown along with GC content by black lines or lines coloured according to the library preparation kits, respectively. Black horizontal lines ( C GC =1) represent unbiased coverage. The data for bins with extreme GC content (those representing

    Article Snippet: Library preparation and sequencing Eight sequencing library preparation kits were used in this study: XT, KAPA HyperPlus (NIPPON Genetics Co. Ltd, Tokyo, Japan) with PCR or PCR-free workflow (referred to as KP and KPF, respectively), NEBNext Ultra II (referred to as NN; New England Biolabs Japan, Tokyo, Japan), QIAseq FX (QS; QIAGEN), TruSeq nano (TS; Illumina), TruSeq DNA PCR-Free (TSF; Illumina), and Nextera DNA Flex (FL; Illumina) ( ).

    Techniques: Sequencing

    Restricted glycolysis enhances the SCLC cell population in breast cancer cells (A) Mammosphere assay. 8-10 days after plating in mammosphere culture conditions, representative images were captured by microscopy (bar 100 μm) and mammospheres were measured by alamarBlue. (one sample t -test). (B) ALDEFLUOR assay; diethylaminobenzaldehyde (DEAB), was used to establish the baseline fluorescence. Flow cytometry plots indicate side scatter (SSC) versus fluorescence intensity. (C) Flow cytometric assessment of surface CD24 and CD44 expression. (B, C) representative of one of three biological repeats. (D) Colony assay; 18 h after plating, media was replaced with media containing either DMSO carrier control or paclitaxel (5 nM) and cells allowed to grow for 8-10 days. (one way ANOVA and Fisher’s LSD test).

    Journal: Oncotarget

    Article Title: The effects of restricted glycolysis on stem-cell like characteristics of breast cancer cells

    doi: 10.18632/oncotarget.25299

    Figure Lengend Snippet: Restricted glycolysis enhances the SCLC cell population in breast cancer cells (A) Mammosphere assay. 8-10 days after plating in mammosphere culture conditions, representative images were captured by microscopy (bar 100 μm) and mammospheres were measured by alamarBlue. (one sample t -test). (B) ALDEFLUOR assay; diethylaminobenzaldehyde (DEAB), was used to establish the baseline fluorescence. Flow cytometry plots indicate side scatter (SSC) versus fluorescence intensity. (C) Flow cytometric assessment of surface CD24 and CD44 expression. (B, C) representative of one of three biological repeats. (D) Colony assay; 18 h after plating, media was replaced with media containing either DMSO carrier control or paclitaxel (5 nM) and cells allowed to grow for 8-10 days. (one way ANOVA and Fisher’s LSD test).

    Article Snippet: After 7-8 days, cell proliferation was measured by alamarBlue (Life Technology, CA, USA).

    Techniques: Microscopy, Fluorescence, Flow Cytometry, Cytometry, Expressing, Colony Assay

    Comparison of Ca i 2+ transients measured using high-affinity dye Fluo-4 (site 1, green traces) and low-affinity dye Fluo-4FF (site 2, red traces), and corresponding V m recordings (blue traces) at different CLs ( A–D ). Green dashed lines duplicate

    Journal: American Journal of Physiology - Heart and Circulatory Physiology

    Article Title: The role of dye affinity in optical measurements of Cai2+ transients in cardiac muscle

    doi: 10.1152/ajpheart.00751.2013

    Figure Lengend Snippet: Comparison of Ca i 2+ transients measured using high-affinity dye Fluo-4 (site 1, green traces) and low-affinity dye Fluo-4FF (site 2, red traces), and corresponding V m recordings (blue traces) at different CLs ( A–D ). Green dashed lines duplicate

    Article Snippet: Several high-affinity dyes were tested including Fluo-4 (Invitrogen), its analog Fluo-2 medium affinity (Fluo-2MA; Teflabs, Austin, TX), and Rhod-2 (Invitrogen and Teflabs).

    Techniques:

    Superimposed Ca i 2+ traces measured with Fluo-4FF, Rhod-2, and Fluo-4 at different CLs. Traces are individually normalized.

    Journal: American Journal of Physiology - Heart and Circulatory Physiology

    Article Title: The role of dye affinity in optical measurements of Cai2+ transients in cardiac muscle

    doi: 10.1152/ajpheart.00751.2013

    Figure Lengend Snippet: Superimposed Ca i 2+ traces measured with Fluo-4FF, Rhod-2, and Fluo-4 at different CLs. Traces are individually normalized.

    Article Snippet: Several high-affinity dyes were tested including Fluo-4 (Invitrogen), its analog Fluo-2 medium affinity (Fluo-2MA; Teflabs, Austin, TX), and Rhod-2 (Invitrogen and Teflabs).

    Techniques: