dna library preparation  (Illumina Inc)

 
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    Name:
    TruSeq DNA Library Prep
    Description:
    The TruSeq Exome Kit previously known as the TruSeq Exome Library Prep Kit is a cost effective library preparation and exome enrichment solution that offers Modular product ordering for low cost exome sequencing Mechanical shearing and TruSeq enrichment technology that yield uniform coverage and high on target sequencing reads A fully supported workflow solution to simplify exome sequencing Cost Effective Exome Sequencing The TruSeq Exome Kit supports 12 plex pre enrichment library pooling enabling researchers to maximize sequencing throughput and variant identification by sequencing up to 12 libraries per flow cell lane This enables sequencing of more exomes per run so researchers can maximize their budgets To learn more about calculating coverage estimates see the sequencing coverage calculator Proven TruSeq Data Quality The TruSeq Exome Kit delivers 80 of on target sequencing reads for efficient cost effective exome sequencing By combining the TruSeq Exome Kit with Illumina systems using sequencing by synthesis SBS technology researchers can identify true coding variants and minimize false positive and false negative calls Convenient Integrated Workflow Solution Illumina provides an integrated supported workflow solution that guides researchers from library preparation through analysis All components of the exome sequencing workflow are designed optimized and analytically validated together Expert Illumina scientists provide a single source of technical and field support for every step in the process Illumina now offers modular product ordering to enable flexibility in your workflows Find automation vendors with robotic systems compatible with this product
    Catalog Number:
    20020181
    Price:
    None
    Category:
    Library Preparation Kits
    Buy from Supplier


    Structured Review

    Illumina Inc dna library preparation
    TruSeq DNA Library Prep
    The TruSeq Exome Kit previously known as the TruSeq Exome Library Prep Kit is a cost effective library preparation and exome enrichment solution that offers Modular product ordering for low cost exome sequencing Mechanical shearing and TruSeq enrichment technology that yield uniform coverage and high on target sequencing reads A fully supported workflow solution to simplify exome sequencing Cost Effective Exome Sequencing The TruSeq Exome Kit supports 12 plex pre enrichment library pooling enabling researchers to maximize sequencing throughput and variant identification by sequencing up to 12 libraries per flow cell lane This enables sequencing of more exomes per run so researchers can maximize their budgets To learn more about calculating coverage estimates see the sequencing coverage calculator Proven TruSeq Data Quality The TruSeq Exome Kit delivers 80 of on target sequencing reads for efficient cost effective exome sequencing By combining the TruSeq Exome Kit with Illumina systems using sequencing by synthesis SBS technology researchers can identify true coding variants and minimize false positive and false negative calls Convenient Integrated Workflow Solution Illumina provides an integrated supported workflow solution that guides researchers from library preparation through analysis All components of the exome sequencing workflow are designed optimized and analytically validated together Expert Illumina scientists provide a single source of technical and field support for every step in the process Illumina now offers modular product ordering to enable flexibility in your workflows Find automation vendors with robotic systems compatible with this product
    https://www.bioz.com/result/dna library preparation/product/Illumina Inc
    Average 99 stars, based on 146 article reviews
    Price from $9.99 to $1999.99
    dna library preparation - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer"

    Article Title: Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer

    Journal: Scientific Reports

    doi: 10.1038/srep33318

    Optimization of the DNA library generation by introducing decoy PCR primers to produce full-length influenza A/H3N2 sequences with even coverage. ( a ) The existing protocol for Nextera XT library preparation on targeted amplicons. Low sequencing read depths were typically found at both 5′ and 3′ ends of the amplicons. ( b ) The direct integration of the transposon sequences to the Tuni-12 and Tuni-13 primer sequences and inclusion of decoy primers during the initial genome-wide PCR before the Nextera XT library preparation. This increases the read depths at both ends of the amplicons.
    Figure Legend Snippet: Optimization of the DNA library generation by introducing decoy PCR primers to produce full-length influenza A/H3N2 sequences with even coverage. ( a ) The existing protocol for Nextera XT library preparation on targeted amplicons. Low sequencing read depths were typically found at both 5′ and 3′ ends of the amplicons. ( b ) The direct integration of the transposon sequences to the Tuni-12 and Tuni-13 primer sequences and inclusion of decoy primers during the initial genome-wide PCR before the Nextera XT library preparation. This increases the read depths at both ends of the amplicons.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Genome Wide

    2) Product Images from "Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA"

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-34079-2

    Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.
    Figure Legend Snippet: Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.

    Techniques Used: Genome Wide, Polymerase Chain Reaction, Produced, Generated, Incubation, Selection

    Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.
    Figure Legend Snippet: Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Generated, Produced, Purification, Incubation

    Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.
    Figure Legend Snippet: Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.

    Techniques Used: Conjugation Assay, Magnetic Beads, Sequencing, Modification, Amplification, Polymerase Chain Reaction, Purification, Selection

    3) Product Images from "Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA"

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-34079-2

    Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.
    Figure Legend Snippet: Genome-wide base composition bias curves in Illumina reads from PCR-free human DNA libraries. ( a ) The GC-bias curves from libraries (in duplicate) produced by the immobilized enzyme method (IM-1 and IM-2 in blue), for end repair for 30 min at 20 °C and 3′ A-tailing at 37 °C in contrast to the data from the libraries generated by the soluble enzyme method, with 3′ A-tailing at 65 °C, using enzyme mixture PKT (PKT-1 and PKT-2 in purple). ( b ) The GC-bias data of the immobilized enzyme method compared to the data from the duplicate libraries generated by Illumina TruSeq DNA PCR-free LT Library Preparation Kit (Illumina), Kapa Hyper Prep Kit (Kapa) or NEBNext Ultra II DNA Library Prep Kit for Illumina (Ultra) according to the protocols of the manufacturers. The Illumina protocol carries out end repair for 30 min at 30 °C and 3′ A-tailing for 30 min at 37 °C, followed by incubation at 70 °C for 5 min, and includes a clean-up and size selection step between end repair and 3′ A-tailing. The Kapa Hyper and NEBNext Ultra workflows include an enzyme mixture to perform end repair for 30 min at 20 °C, followed by 3′ A-tailing for 30 min at 65 °C.

    Techniques Used: Genome Wide, Polymerase Chain Reaction, Produced, Generated, Incubation, Selection

    Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.
    Figure Legend Snippet: Effect of end repair and 3′ A-tailing at high temperature on GC-bias in Illumina reads from PCR-free human DNA libraries. ( a ) Comparison of GC-bias curves in duplicate libraries prepared by immobilized enzymes with 3′ A-tailing performed at 37 °C (IM 37 °C -1 and IM 37 °C -2, in blue) or 65 °C (IM 65 °C -1 and IM 65 °C -2, in green) revealed a dramatic effect of 3′ A-tailing at high temperature on sequence coverage of the AT-rich regions from human DNA libraries. ( b ) GC-bias curves were generated from two sets of duplicate libraries produced using the soluble enzyme mixture PKT with (PKT purify-1 and PKT purify-2) or without (PKT-1 and PKT-2) a purification step between end repair and high temperature incubation (with Taq DNA pol added to the samples following purification). Although some bias against AT-rich regions can be attributed to the end repair step, the elevated temperature contributes to the majority of the dropouts in the AT-rich regions. ( c ) Shown are the GC-bias curves from 4 sets of duplicate libraries produced by the method of soluble enzymes. Two sets of the duplicate libraries were purified after end repair with PK mixture and then treated at 37 °C with Klenow Fragment (3′-5′ exo − ) (red, Klenow 37 °C-1 and Klenow 37 °C-2) or Taq DNA pol (blue, Taq 37 °C-1 and Taq 37 °C-2). The other two duplicate sets were prepared using the high temperature treatment protocol either with (green, Taq 65 °C-1 and Taq 65 °C-2) or without (orange, PKT-1 and PKT-2) a purification step between end repair with PKT and treatment with Taq DNA pol at 65 °C for 30 min. ( d ) Comparison of library yield of the three sets described above with or without (PKT on the left) a purification step between end repair and 3′ A-tailing indicates that purification caused substantial loss of library DNA.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Generated, Produced, Purification, Incubation

    Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 -benzylguanine (BG) moieties that specifically react with active site cysteine residues of SNAP-tag proteins, forming a stable covalent thioether bond 15 , 16 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.
    Figure Legend Snippet: Enzyme immobilization and comparison of Illumina library preparation protocols. ( a ) A schematic of covalent conjugation of SNAP-tagged enzyme fusion proteins to magnetic beads functionalized with O 6 -benzylguanine (BG) moieties that specifically react with active site cysteine residues of SNAP-tag proteins, forming a stable covalent thioether bond 15 , 16 . ( b ) Workflow for library construction using immobilized enzymes for Illumina sequencing. A typical streamlined protocol for Illumina library construction is modified by employing immobilized enzymes to catalyze end repair and 3′ A-tailing. This method utilizes SNAP-tagged T4 DNA pol and PNK covalently conjugated to BG-functionalized magnetic beads to carry out end repair of fragmented DNA at 20°C (or 37 °C) for 30 min. The enzymes are removed by magnetic separation from the DNA pool, which is subjected to 3′ A-tailing at 37 °C for 30 min using immobilized Taq DNA pol. ( c ) Streamlined protocol for Illumina amplification-free library preparation using soluble enzymes. Typically, end repair and 3′ A-tailing of fragmented DNA are catalyzed by an enzyme mixture at 20 °C for 30 min, followed by heat treatment at 65 °C for 30 min. ( d ) The workflow of Illumina TruSeq DNA PCR-free LT Library Prep Kit with a purification step. End repair is performed for 30 min at 30 °C, followed by a bead-based step for clean up and size selection. 3′ A-tailing is carried out for 30 min at 37 °C with a subsequent treatment for 5 min at 70 °C. Each library was ligated to preannealed full-length paired-end Illumina adaptors, size-selected and analyzed, and sequenced on an Illumina sequencing platform.

    Techniques Used: Conjugation Assay, Magnetic Beads, Sequencing, Modification, Amplification, Polymerase Chain Reaction, Purification, Selection

    4) Product Images from "A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing"

    Article Title: A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0068988

    Integrated microfluidic system for preparing DNA libraries for sequencing. a) Top view of an integrated system and side view of the DMF-capillary interface, which features a central DMF hub for integrating multiple reagent and sample preparation modules (depicted in different colors), magnets and thermal blocks coupled to module tubing for sample preparation, and multi-valve syringe pumps for liquid handling. b) Schematic (left) of a DMF device showing the arrangement of indium tin oxide (ITO) actuation electrodes used to route samples and reagents to and from the capillaries, which are responsible for transferring liquids to their respective modules. Sequence of frames (right) from a movie illustratfing the stages in preparing a sequencer-ready DNA library using the microfluidic method (note that off-DMF processing is not shown in the perspective of the frames): (1) Mixing of gDNA (1.8 µL) and Nextera Enzyme (NE, 0.6 µL) droplets; (2,3) post-tagmentation droplet (gDNA+NE reaction products) merged with magnetic bead (MB) droplet (4.5 µL) and actuated to clean-up module; (4,5) post-clean-up droplet (2.2 µL) of purified DNA fragments actuated to PCR Mix droplet (2.8 µL) for limited-cycle PCR; (6,7) post-PCR DNA fragment droplet mixed with different volumes (2.2 and 0.45 µL) of magnetic beads for size-selection; and (8) DNA library droplet (3 µL).
    Figure Legend Snippet: Integrated microfluidic system for preparing DNA libraries for sequencing. a) Top view of an integrated system and side view of the DMF-capillary interface, which features a central DMF hub for integrating multiple reagent and sample preparation modules (depicted in different colors), magnets and thermal blocks coupled to module tubing for sample preparation, and multi-valve syringe pumps for liquid handling. b) Schematic (left) of a DMF device showing the arrangement of indium tin oxide (ITO) actuation electrodes used to route samples and reagents to and from the capillaries, which are responsible for transferring liquids to their respective modules. Sequence of frames (right) from a movie illustratfing the stages in preparing a sequencer-ready DNA library using the microfluidic method (note that off-DMF processing is not shown in the perspective of the frames): (1) Mixing of gDNA (1.8 µL) and Nextera Enzyme (NE, 0.6 µL) droplets; (2,3) post-tagmentation droplet (gDNA+NE reaction products) merged with magnetic bead (MB) droplet (4.5 µL) and actuated to clean-up module; (4,5) post-clean-up droplet (2.2 µL) of purified DNA fragments actuated to PCR Mix droplet (2.8 µL) for limited-cycle PCR; (6,7) post-PCR DNA fragment droplet mixed with different volumes (2.2 and 0.45 µL) of magnetic beads for size-selection; and (8) DNA library droplet (3 µL).

    Techniques Used: Sequencing, Sample Prep, Transferring, Purification, Polymerase Chain Reaction, Magnetic Beads, Selection

    Nextera® protocol for preparing DNA libraries compatible with Illumina sequencers. Key steps include: gDNA tagmentation, clean-up, limited-cycle PCR, and selection of size-specific DNA library for sequencing and analysis.
    Figure Legend Snippet: Nextera® protocol for preparing DNA libraries compatible with Illumina sequencers. Key steps include: gDNA tagmentation, clean-up, limited-cycle PCR, and selection of size-specific DNA library for sequencing and analysis.

    Techniques Used: Polymerase Chain Reaction, Selection, Sequencing

    5) Product Images from "A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing"

    Article Title: A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0068988

    Integrated microfluidic system for preparing DNA libraries for sequencing. a) Top view of an integrated system and side view of the DMF-capillary interface, which features a central DMF hub for integrating multiple reagent and sample preparation modules (depicted in different colors), magnets and thermal blocks coupled to module tubing for sample preparation, and multi-valve syringe pumps for liquid handling. b) Schematic (left) of a DMF device showing the arrangement of indium tin oxide (ITO) actuation electrodes used to route samples and reagents to and from the capillaries, which are responsible for transferring liquids to their respective modules. Sequence of frames (right) from a movie illustratfing the stages in preparing a sequencer-ready DNA library using the microfluidic method (note that off-DMF processing is not shown in the perspective of the frames): (1) Mixing of gDNA (1.8 µL) and Nextera Enzyme (NE, 0.6 µL) droplets; (2,3) post-tagmentation droplet (gDNA+NE reaction products) merged with magnetic bead (MB) droplet (4.5 µL) and actuated to clean-up module; (4,5) post-clean-up droplet (2.2 µL) of purified DNA fragments actuated to PCR Mix droplet (2.8 µL) for limited-cycle PCR; (6,7) post-PCR DNA fragment droplet mixed with different volumes (2.2 and 0.45 µL) of magnetic beads for size-selection; and (8) DNA library droplet (3 µL).
    Figure Legend Snippet: Integrated microfluidic system for preparing DNA libraries for sequencing. a) Top view of an integrated system and side view of the DMF-capillary interface, which features a central DMF hub for integrating multiple reagent and sample preparation modules (depicted in different colors), magnets and thermal blocks coupled to module tubing for sample preparation, and multi-valve syringe pumps for liquid handling. b) Schematic (left) of a DMF device showing the arrangement of indium tin oxide (ITO) actuation electrodes used to route samples and reagents to and from the capillaries, which are responsible for transferring liquids to their respective modules. Sequence of frames (right) from a movie illustratfing the stages in preparing a sequencer-ready DNA library using the microfluidic method (note that off-DMF processing is not shown in the perspective of the frames): (1) Mixing of gDNA (1.8 µL) and Nextera Enzyme (NE, 0.6 µL) droplets; (2,3) post-tagmentation droplet (gDNA+NE reaction products) merged with magnetic bead (MB) droplet (4.5 µL) and actuated to clean-up module; (4,5) post-clean-up droplet (2.2 µL) of purified DNA fragments actuated to PCR Mix droplet (2.8 µL) for limited-cycle PCR; (6,7) post-PCR DNA fragment droplet mixed with different volumes (2.2 and 0.45 µL) of magnetic beads for size-selection; and (8) DNA library droplet (3 µL).

    Techniques Used: Sequencing, Sample Prep, Transferring, Purification, Polymerase Chain Reaction, Magnetic Beads, Selection

    Nextera® protocol for preparing DNA libraries compatible with Illumina sequencers. Key steps include: gDNA tagmentation, clean-up, limited-cycle PCR, and selection of size-specific DNA library for sequencing and analysis.
    Figure Legend Snippet: Nextera® protocol for preparing DNA libraries compatible with Illumina sequencers. Key steps include: gDNA tagmentation, clean-up, limited-cycle PCR, and selection of size-specific DNA library for sequencing and analysis.

    Techniques Used: Polymerase Chain Reaction, Selection, Sequencing

    6) Product Images from "Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer"

    Article Title: Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer

    Journal: Scientific Reports

    doi: 10.1038/srep33318

    Optimization of the DNA library generation by introducing decoy PCR primers to produce full-length influenza A/H3N2 sequences with even coverage. ( a ) The existing protocol for Nextera XT library preparation on targeted amplicons. Low sequencing read depths were typically found at both 5′ and 3′ ends of the amplicons. ( b ) The direct integration of the transposon sequences to the Tuni-12 and Tuni-13 primer sequences and inclusion of decoy primers during the initial genome-wide PCR before the Nextera XT library preparation. This increases the read depths at both ends of the amplicons.
    Figure Legend Snippet: Optimization of the DNA library generation by introducing decoy PCR primers to produce full-length influenza A/H3N2 sequences with even coverage. ( a ) The existing protocol for Nextera XT library preparation on targeted amplicons. Low sequencing read depths were typically found at both 5′ and 3′ ends of the amplicons. ( b ) The direct integration of the transposon sequences to the Tuni-12 and Tuni-13 primer sequences and inclusion of decoy primers during the initial genome-wide PCR before the Nextera XT library preparation. This increases the read depths at both ends of the amplicons.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Genome Wide

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    Sequencing:

    Article Title: Mung Bean Nuclease Treatment Increases Capture Specificity of Microdroplet-PCR Based Targeted DNA Enrichment
    Article Snippet: .. Concatenation of enriched DNA, TruSeq library prep and sequencing using the Illumina Miseq For end repair, 100 ng of enrichment products, either treated or untreated with mung bean nuclease, were mixed with 10 µl of NEBNext end repair buffer (New England Biolabs), 5 µl of NEBNext end repair enzyme mix (New England Biolabs) and nuclease-free water to bring to a final reaction volume of 100 µl. .. End repair reaction was incubated at 37°C for 20 min. End-repaired DNA was purified using 150 µl of Agencourt Ampure XP beads (Beckman Coulter) following manufacturer's instructions and eluted in 37.5 µl of nuclease-free water.

    Article Title: Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results
    Article Snippet: .. Currently, the Illumina TruSeq® DNA library preparation kit represents one of the most widely used solutions for the generation of paired-end genome sequencing libraries. ..

    Article Title: Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing
    Article Snippet: .. Genome library construction and sequencing Genomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products. .. Genome library construction and sequencingGenomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products.

    Article Title: Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results
    Article Snippet: .. On the contrary, for DNA samples higher base count and sequencing coverage values were achieved preparing libraries using TruSeq Nano DNA Library Prep in comparison to Nextera XT DNA Library Preparation Kit (482.28 vs 368.45 Mbp; 117 vs 89.59 fold) ( ). .. The two-way ANOVA analysis revealed that changes in base count and coverage were not significantly affected by the library preparation kit (P = 0.73 and 0.71, respectively) as well as by DNA extraction procedures (P = 0.65 and 0.56, respectively) with reference to the DNA extraction protocols applied both on BACT and DNA samples.

    Generated:

    Article Title: Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Article Snippet: .. Library preparationSynthetic long-read libraries were generated for the AJ Trio and Chinese Trio using the TruSeq Synthetic Long-Read DNA Library Prep Kit (Illumina, Cat# FC-126–1001). .. 500 ng of DNA from the NIST Reference Materials (or from Coriell for the Chinese parents) was sheared, end-repaired, A-tailed, and adapters ligated before size-selecting 9–11 kb fragments according to the manufacturer’s protocol (Illumina Part # 15047264 Rev.

    Amplification:

    Article Title: Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing
    Article Snippet: .. Genome library construction and sequencing Genomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products. .. Genome library construction and sequencingGenomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products.

    Sample Prep:

    Article Title: Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing
    Article Snippet: .. Genome library construction and sequencing Genomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products. .. Genome library construction and sequencingGenomic libraries were prepared using Illumina TruSeq DNA Sample Prep kits (Illumina, Inc., CA, US) without an amplification step to produce the final products.

    other:

    Article Title: Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results
    Article Snippet: Libraries prepared using TruSeq Nano DNA Library Prep were sequenced with the MiSeq platform only.

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