Selected article for: "library preparation and ng library"
Author: Nathan D. Grubaugh; Sharada Saraf; Karthik Gangavarapu; Alexander Watts; Amanda L. Tan; Rachel J. Oidtman; Jason T. Ladner; Glenn Oliveira; Nathaniel L. Matteson; Moritz U.G. Kraemer; Chantal B.F. Vogels; Aaron Hentoff; Deepit Bhatia; Danielle Stanek; Blake Scott; Vanessa Landis; Ian Stryker; Marshall R. Cone; Edgar W. Kopp; Andrew C. Cannons; Lea Heberlein-Larson; Stephen White; Leah D. Gillis; Michael J. Ricciardi; Jaclyn Kwal; Paola K. Lichtenberger; Diogo M. Magnani; David I. Watkins; Gustavo Palacios; Davidson H. Hamer; Lauren M. Gardner; T. Alex Perkins; Guy Baele; Kamran Khan; Andrea Morrison; Sharon Isern; Scott F. Michael; Kristian G. Andersen
Title: International travelers and genomics uncover a ‘hidden’ Zika outbreak
  • Document date: 2018_12_14
    • ID: lh6zul8l_60
    Snippet: Zika virus RNA was sequenced using a highly multiplexed PCR approach, called PrimalSeq, that we previously described (Grubaugh et al., 2018b; Quick et al., 2017) . Detailed protocols, including the primer scheme "ZIKV -Asia/America -400bp" we used here to amplify Zika virus, can be found online (http://grubaughlab.com/openscience/amplicon-sequencing/ and https://andersenlab.com/secrets/protocols/). In brief, virus RNA (2 μL) was reverse transcri.....
    Document: Zika virus RNA was sequenced using a highly multiplexed PCR approach, called PrimalSeq, that we previously described (Grubaugh et al., 2018b; Quick et al., 2017) . Detailed protocols, including the primer scheme "ZIKV -Asia/America -400bp" we used here to amplify Zika virus, can be found online (http://grubaughlab.com/openscience/amplicon-sequencing/ and https://andersenlab.com/secrets/protocols/). In brief, virus RNA (2 μL) was reverse transcribed into cDNA using Invitrogen SuperScript IV VILO (20 µL reactions). Virus cDNA (2 μL) was amplified in 35 × ~400 bp fragments from two multiplexed PCR reactions using Q5 DNA High-fidelity Polymerase (New England Biolabs). Virus amplicons from the two multiplex PCR reactions were purified and combined (25 ng each) prior to library preparation. The libraries were prepared using the Kapa Hyper prep kit (Kapa Biosystems, following the vendor's protocols but with ¼ of the recommended reagents) and NEXTflex Dual-Indexed DNA Barcodes (BIOO Scientific, diluted to 250 nM). Mag-Bind TotalPure NGS beads (Omega) were used for all purification steps. The libraries were quantified and quality-checked using the Qubit (Thermo Fisher) and Bioanalyzer (Agilent). Paired-end 250 nt reads were generated using the MiSeq V2 500 cycle kits (Illumina).

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