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    Illumina Inc nextera xt kit
    Heatmap noting the completeness of genomic bins extracted from each of the low input metagenomes. The color bar on top of the figure refers to each of the three tested library types and control library (Control = red, <t>Nextera</t> XT = green, Mondrian = blue and MALBAC = yellow). Samples are also arranged where the highest input quantity is located on the left side of each library type
    Nextera Xt Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 6108 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextera xt kit/product/Illumina Inc
    Average 99 stars, based on 6108 article reviews
    Price from $9.99 to $1999.99
    nextera xt kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    90
    Illumina Inc nextera xt index kit v2
    Heatmap noting the completeness of genomic bins extracted from each of the low input metagenomes. The color bar on top of the figure refers to each of the three tested library types and control library (Control = red, <t>Nextera</t> XT = green, Mondrian = blue and MALBAC = yellow). Samples are also arranged where the highest input quantity is located on the left side of each library type
    Nextera Xt Index Kit V2, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 390 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nextera xt index kit v2/product/Illumina Inc
    Average 90 stars, based on 390 article reviews
    Price from $9.99 to $1999.99
    nextera xt index kit v2 - by Bioz Stars, 2020-09
    90/100 stars
      Buy from Supplier

    Image Search Results


    Heatmap noting the completeness of genomic bins extracted from each of the low input metagenomes. The color bar on top of the figure refers to each of the three tested library types and control library (Control = red, Nextera XT = green, Mondrian = blue and MALBAC = yellow). Samples are also arranged where the highest input quantity is located on the left side of each library type

    Journal: BMC Genomics

    Article Title: Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

    doi: 10.1186/s12864-015-2063-6

    Figure Lengend Snippet: Heatmap noting the completeness of genomic bins extracted from each of the low input metagenomes. The color bar on top of the figure refers to each of the three tested library types and control library (Control = red, Nextera XT = green, Mondrian = blue and MALBAC = yellow). Samples are also arranged where the highest input quantity is located on the left side of each library type

    Article Snippet: Two low template library preparation methods that may be amenable to higher throughput are Illumina’s Nextera XT kit and NuGEN’s Mondrian microfluidics workstation in conjunction with the NuGEN Ovation library preparation kit.

    Techniques: Multiple Annealing and Looping–Based Amplification Cycles

    Graphical summary of the SL-seq protocol. (A) cDNA generation with Superscript III and a primer that is partially random (7 nucleotides, grey), and partially fixed (yellow). Consequent degradation of the RNA strand with RNAse H, leaving a single stranded DNA molecule. (B) Second strand synthesis of SL-containing DNA molecules with Klenow fragment and a primer that is complementary with the SL (dark blue). (C + D) PCR for amplification and addition of adapter motives (red and purple) making the library compatible with the Nextera XT index kit (Illumina). (E + F) Final PCR adapter extension, indexing (orange and light blue) and amplification of the library fragments with the primers of the Nextera XT index kit. Dark Blue: SL/ complementary with SL, light grey: RNA, dark grey: DNA, green: poly-A tail. Other colors: primer and adapters sequences.

    Journal: Scientific Reports

    Article Title: Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids

    doi: 10.1038/s41598-017-03987-0

    Figure Lengend Snippet: Graphical summary of the SL-seq protocol. (A) cDNA generation with Superscript III and a primer that is partially random (7 nucleotides, grey), and partially fixed (yellow). Consequent degradation of the RNA strand with RNAse H, leaving a single stranded DNA molecule. (B) Second strand synthesis of SL-containing DNA molecules with Klenow fragment and a primer that is complementary with the SL (dark blue). (C + D) PCR for amplification and addition of adapter motives (red and purple) making the library compatible with the Nextera XT index kit (Illumina). (E + F) Final PCR adapter extension, indexing (orange and light blue) and amplification of the library fragments with the primers of the Nextera XT index kit. Dark Blue: SL/ complementary with SL, light grey: RNA, dark grey: DNA, green: poly-A tail. Other colors: primer and adapters sequences.

    Article Snippet: Addition of Illumina adapters, amplification and sample indexing Additional adapter sequences were added on 5′ and 3′ end of the library fragments to make them compatible with the Nextera XT Index Kit (Illumina).

    Techniques: Polymerase Chain Reaction, Amplification

    The assay design is based on various steps: (1) In the present study, sampling cell collection was performed at two different moments: before any cancer treatment and during patient follow-up almost 6 months after OSCC treatment; (2) DNA purification and bisulfite treatment (unmethylated cytosines are chemically converted to uracils, while methylated cytosines remained unchanged); (3) Target-specific amplification of 13-gene panel ( ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MIR193, LINC00599, MIR296, TERT , and GP1BB ) and barcoding using Nextera™ index kit (Illumina); (4) PCR purification, quantification and pooling; (5) loading onto MiSEQ; (6) DNA methylation level of a series of 243 CpGs representatives of the 13-gene promoters was calculated in cloud computing using different web tools: BSPAT, BWAmeth, MethylDackel, Kismeth and finally EPIC-TABSAT; (7) score calculation: An algorithm of choice was used to calculate the final score of each sample. This was done multiplying the DNA methylation level of the most informative CpGs previously identified for the corresponding coefficient and adding the constant (see Morandi et al. for details [ 15 ]).

    Journal: Journal of Clinical Medicine

    Article Title: 13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients

    doi: 10.3390/jcm8122107

    Figure Lengend Snippet: The assay design is based on various steps: (1) In the present study, sampling cell collection was performed at two different moments: before any cancer treatment and during patient follow-up almost 6 months after OSCC treatment; (2) DNA purification and bisulfite treatment (unmethylated cytosines are chemically converted to uracils, while methylated cytosines remained unchanged); (3) Target-specific amplification of 13-gene panel ( ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MIR193, LINC00599, MIR296, TERT , and GP1BB ) and barcoding using Nextera™ index kit (Illumina); (4) PCR purification, quantification and pooling; (5) loading onto MiSEQ; (6) DNA methylation level of a series of 243 CpGs representatives of the 13-gene promoters was calculated in cloud computing using different web tools: BSPAT, BWAmeth, MethylDackel, Kismeth and finally EPIC-TABSAT; (7) score calculation: An algorithm of choice was used to calculate the final score of each sample. This was done multiplying the DNA methylation level of the most informative CpGs previously identified for the corresponding coefficient and adding the constant (see Morandi et al. for details [ 15 ]).

    Article Snippet: Libraries were prepared using the Nextera™ Index Kit (Illumina, San Diego, CA, USA) by a locus-specific bisulfite amplicon approach [ ] and loaded onto MiSEQ (Illumina, San Diego, CA, USA, cod.

    Techniques: Sampling, DNA Purification, Methylation, Amplification, Polymerase Chain Reaction, Purification, DNA Methylation Assay

    Lower limit of starting cDNA for tagmentation libraries. ( A , B ) Bioanalyzer electropherograms of tagmented DNA from reactions using 500 pg to 0.1 pg cDNA using either Nextera XT ( A ) or in-house Tn5 and reaction conditions including TAPS buffer and 8% PEG

    Journal: Genome Research

    Article Title: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

    doi: 10.1101/gr.177881.114

    Figure Lengend Snippet: Lower limit of starting cDNA for tagmentation libraries. ( A , B ) Bioanalyzer electropherograms of tagmented DNA from reactions using 500 pg to 0.1 pg cDNA using either Nextera XT ( A ) or in-house Tn5 and reaction conditions including TAPS buffer and 8% PEG

    Article Snippet: Elution was performed with 25 μL of resuspension buffer (RSB) from the Nextera kit, and 20 μL was used for the final enrichment PCR along with 15 μL of Nextera PCR master mix (NPM), 5 μL of Index 1 primers (N7xx), 5 μL of Index 2 primers (N5xx), and 5 μL of PCR primer cocktail (PPC; composed of FC-121-1012 and FC-121-1011 primers; see Illumina website).

    Techniques:

    Tagmentation reactions with molecular crowding agents. ( A ) Bioanalyzer electropherograms of tagmented DNA from reactions with different concentrations of PEG 8000 or no PEG or using Nextera XT reaction conditions. ( B ) Bioanalyzer electropherograms of

    Journal: Genome Research

    Article Title: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

    doi: 10.1101/gr.177881.114

    Figure Lengend Snippet: Tagmentation reactions with molecular crowding agents. ( A ) Bioanalyzer electropherograms of tagmented DNA from reactions with different concentrations of PEG 8000 or no PEG or using Nextera XT reaction conditions. ( B ) Bioanalyzer electropherograms of

    Article Snippet: Elution was performed with 25 μL of resuspension buffer (RSB) from the Nextera kit, and 20 μL was used for the final enrichment PCR along with 15 μL of Nextera PCR master mix (NPM), 5 μL of Index 1 primers (N7xx), 5 μL of Index 2 primers (N5xx), and 5 μL of PCR primer cocktail (PPC; composed of FC-121-1012 and FC-121-1011 primers; see Illumina website).

    Techniques:

    Efficient and robust tagmentation reactions. ( A ) Bioanalyzer electropherograms of tagmented DNA libraries using Nextera (with column purification), in-house Tn5, and buffers with and without column purification. ( B ) Bioanalyzer electropherograms of tagmented

    Journal: Genome Research

    Article Title: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

    doi: 10.1101/gr.177881.114

    Figure Lengend Snippet: Efficient and robust tagmentation reactions. ( A ) Bioanalyzer electropherograms of tagmented DNA libraries using Nextera (with column purification), in-house Tn5, and buffers with and without column purification. ( B ) Bioanalyzer electropherograms of tagmented

    Article Snippet: Elution was performed with 25 μL of resuspension buffer (RSB) from the Nextera kit, and 20 μL was used for the final enrichment PCR along with 15 μL of Nextera PCR master mix (NPM), 5 μL of Index 1 primers (N7xx), 5 μL of Index 2 primers (N5xx), and 5 μL of PCR primer cocktail (PPC; composed of FC-121-1012 and FC-121-1011 primers; see Illumina website).

    Techniques: Purification

    Experimental scheme. ( A ) After differentiation, the cell cultures were dissociated to single-cell suspensions and loaded onto a Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq. On the arrays, the cells were lysed, and reverse transcription of the mRNA and PCR amplification of the cDNA were performed using the C1 Single-Cell Auto Prep System (Fluidigm). Libraries were then prepared using the Nextera XT DNA Library Prep Kit and mosquito HTS liquid handler (TTP). For the final PCR reactions, we used a Bio-Rad 384 Thermal Cycler. Libraries were pooled and sequenced on an Illumina HiSeq 2500. ( B ) WA09 human embryonic stem cells were differentiated in vitro to the pancreatic lineage. Cells from stages 1 and 2 were collected and analyzed using the procedures outlined in A . Two independent cells from stage 1 (cell A and cell B) and two cells from stage 2 (cell C and cell D) were selected and yielded with similar cDNA concentrations (mean [SD] concentration = 0.38 [0.04] ng/µL). For library preparation, we tested 2-µL, 4-µL, and 8-µL final volume reactions, with four replicates per reaction volume.

    Journal: Jala (Charlottesville, Va.)

    Article Title: Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing

    doi: 10.1177/2211068216630741

    Figure Lengend Snippet: Experimental scheme. ( A ) After differentiation, the cell cultures were dissociated to single-cell suspensions and loaded onto a Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq. On the arrays, the cells were lysed, and reverse transcription of the mRNA and PCR amplification of the cDNA were performed using the C1 Single-Cell Auto Prep System (Fluidigm). Libraries were then prepared using the Nextera XT DNA Library Prep Kit and mosquito HTS liquid handler (TTP). For the final PCR reactions, we used a Bio-Rad 384 Thermal Cycler. Libraries were pooled and sequenced on an Illumina HiSeq 2500. ( B ) WA09 human embryonic stem cells were differentiated in vitro to the pancreatic lineage. Cells from stages 1 and 2 were collected and analyzed using the procedures outlined in A . Two independent cells from stage 1 (cell A and cell B) and two cells from stage 2 (cell C and cell D) were selected and yielded with similar cDNA concentrations (mean [SD] concentration = 0.38 [0.04] ng/µL). For library preparation, we tested 2-µL, 4-µL, and 8-µL final volume reactions, with four replicates per reaction volume.

    Article Snippet: The resulting cDNAs were diluted to a final concentration of 0.1 ng/µL and then converted to Illumina sequencing libraries using the Nextera XT (Illumina) kit using protocols specifically designed for the mosquito HTS (TTP Labtech) (ST2).

    Techniques: Polymerase Chain Reaction, Amplification, In Vitro, Concentration Assay

    Library QC Tape station electropherogram. Nextera Post-PCR libraries constructed with a range of concentrations (post-normalisation) and gDNA from four different genomes: Mycobacterium tuberculosis (purple), Escherichia coli (blue), Clostridium difficile (red) and Plasmodium falciparum (green). Libraries were constructed using the standard Nextera protocol (A) . Evaluation of the Axyprep Mag Normaliser kit (B) : two individual C. difficile Nextera libraries were constructed using the standard Illumina protocol (light/dark green) and two with our normalisation workflow (light/dark purple). Where the standard library had very short inserts, our method produced a library with the normal size distribution. Evaluation of C. difficile Nextera Post-PCR libraries constructed using varying volume Nextera reactions (C) : standard (purple), half-volume (green), quarter-volume (red) and one-eighth volume (blue). Size distribution profiles of libraries constructed using normalisation followed by reaction E (D) : M. tuberculosis (purple), E. coli (blue), C. difficile (red) and P. falciparum (green).

    Journal: BMC Biotechnology

    Article Title: Improved workflows for high throughput library preparation using the transposome-based nextera system

    doi: 10.1186/1472-6750-13-104

    Figure Lengend Snippet: Library QC Tape station electropherogram. Nextera Post-PCR libraries constructed with a range of concentrations (post-normalisation) and gDNA from four different genomes: Mycobacterium tuberculosis (purple), Escherichia coli (blue), Clostridium difficile (red) and Plasmodium falciparum (green). Libraries were constructed using the standard Nextera protocol (A) . Evaluation of the Axyprep Mag Normaliser kit (B) : two individual C. difficile Nextera libraries were constructed using the standard Illumina protocol (light/dark green) and two with our normalisation workflow (light/dark purple). Where the standard library had very short inserts, our method produced a library with the normal size distribution. Evaluation of C. difficile Nextera Post-PCR libraries constructed using varying volume Nextera reactions (C) : standard (purple), half-volume (green), quarter-volume (red) and one-eighth volume (blue). Size distribution profiles of libraries constructed using normalisation followed by reaction E (D) : M. tuberculosis (purple), E. coli (blue), C. difficile (red) and P. falciparum (green).

    Article Snippet: Reduced volume nextera library preparation Nextera libraries were constructed using Clostridium difficile gDNA and the Illumina Nextera™ Kit.

    Techniques: Polymerase Chain Reaction, Construct, Produced

    Quantitative analysis of PACS genome enrichment with next-generation sequencing. Analysis of RB1 and CDKN2A genomic loci for the presence of DU145-specific SNPs. Sequencing libraries from RB1 and CDKN2A amplicons were generated using Nextera XT reagents. ( A ) Quantitative analysis of RB1 sequence reads demonstrated that the DU145-specific nonsense mutation, AAG to TAG (see Figure 4 ), was found in 6.2% of the sequence reads generated from presorted cell lysate. Following PACS sorting (Vim+ PACS) the presence of this mutation relative to the Raji-specific codon was enriched to 87.7%. ( B ) Similar data was obtained upon sequence analysis of CDKN2A amplicons generated from presorted and Vim+ PACS sorted cell lysate. The DU145-specific missense mutation, GAC to TAC (see Figure 4 ), went from comprising 13.5% of the sequence reads to 74.2% of the sequence reads upon PACS enrichment. More than 15 000 sequence reads were analyzed for each of the four samples.

    Journal: Nucleic Acids Research

    Article Title: Identification and genetic analysis of cancer cells with PCR-activated cell sorting

    doi: 10.1093/nar/gku606

    Figure Lengend Snippet: Quantitative analysis of PACS genome enrichment with next-generation sequencing. Analysis of RB1 and CDKN2A genomic loci for the presence of DU145-specific SNPs. Sequencing libraries from RB1 and CDKN2A amplicons were generated using Nextera XT reagents. ( A ) Quantitative analysis of RB1 sequence reads demonstrated that the DU145-specific nonsense mutation, AAG to TAG (see Figure 4 ), was found in 6.2% of the sequence reads generated from presorted cell lysate. Following PACS sorting (Vim+ PACS) the presence of this mutation relative to the Raji-specific codon was enriched to 87.7%. ( B ) Similar data was obtained upon sequence analysis of CDKN2A amplicons generated from presorted and Vim+ PACS sorted cell lysate. The DU145-specific missense mutation, GAC to TAC (see Figure 4 ), went from comprising 13.5% of the sequence reads to 74.2% of the sequence reads upon PACS enrichment. More than 15 000 sequence reads were analyzed for each of the four samples.

    Article Snippet: For next-generation sequencing, 1 ng of each amplicon was subsequently used for sequencing library preparation using the Nextera XT library kit (Illumina).

    Techniques: Next-Generation Sequencing, Sequencing, Generated, Mutagenesis

    Vision 2.6.24 image of 13 illumina nextera XT ® VPRI 18536 DNA extraction protocol libraries mapped to P . leucotricha ITS (GenBank accession no. KX842350.1) including P . tridactyla as an outgroup for comparison. Continuous unbroken lines represent sequence reads that completely align to the reference sequence. Gaps in the alignment indicates no mapping sequence reads, and SNPs between the mapped read and the reference are represented as black bars. Colour code: Grey- P . tridactyla , Dark Blue- CheX (Chelex ® 100), Light Green- InuP (innuPrep Plant DNA), Light Pink- SDS (sodium dodecyl sulphate), Blue- EznS (E.Z.N.A. ® SP Plant), Green- DnaZ (DNAzol ™ ), Yellow- EznF (E.Z.N.A. ® Forensic DNA), Purple- DneP (Qiagen DNeasy ® Plant), Red- IspC (Isolate II Plant DNA Lysis buffer PA1 C), Light Blue- IspS (Isolate II Plant DNA Lysis buffer PA2 S), Dark Green- WizG (Wizard ® Genomic DNA Purification), Light Blue- EznP (E.Z.N.A. ® Plant), Dark Pink- CTAB (Cetyl trimethyl ammonium bromide) and Light Yellow- DneP+ (Qiagen DNeasy ® Plant plus PTB).

    Journal: PLoS ONE

    Article Title: Rediscovering an old foe: Optimised molecular methods for DNA extraction and sequencing applications for fungarium specimens of powdery mildew (Erysiphales)

    doi: 10.1371/journal.pone.0232535

    Figure Lengend Snippet: Vision 2.6.24 image of 13 illumina nextera XT ® VPRI 18536 DNA extraction protocol libraries mapped to P . leucotricha ITS (GenBank accession no. KX842350.1) including P . tridactyla as an outgroup for comparison. Continuous unbroken lines represent sequence reads that completely align to the reference sequence. Gaps in the alignment indicates no mapping sequence reads, and SNPs between the mapped read and the reference are represented as black bars. Colour code: Grey- P . tridactyla , Dark Blue- CheX (Chelex ® 100), Light Green- InuP (innuPrep Plant DNA), Light Pink- SDS (sodium dodecyl sulphate), Blue- EznS (E.Z.N.A. ® SP Plant), Green- DnaZ (DNAzol ™ ), Yellow- EznF (E.Z.N.A. ® Forensic DNA), Purple- DneP (Qiagen DNeasy ® Plant), Red- IspC (Isolate II Plant DNA Lysis buffer PA1 C), Light Blue- IspS (Isolate II Plant DNA Lysis buffer PA2 S), Dark Green- WizG (Wizard ® Genomic DNA Purification), Light Blue- EznP (E.Z.N.A. ® Plant), Dark Pink- CTAB (Cetyl trimethyl ammonium bromide) and Light Yellow- DneP+ (Qiagen DNeasy ® Plant plus PTB).

    Article Snippet: Next generation sequencing VPRI 18536 Two library preparation kits, Illumina Nextera XT® (San Diego, California, USA) and NuGen Ovation® ultralow System V2 (San Carlos, California, USA), were compared using DNA extracts from the 13 DNA extraction protocols applied to VPRI specimen 18536.

    Techniques: DNA Extraction, Sequencing, Lysis, DNA Purification