Next-Generation Sequencing Product Citations Notes Nucleic Acid Extraction Product Used Citation Maxwell® 16 MDx Research Instrument Maxwell® 16 LEV simplyRNA Blood Kit Lozano-Torres et. al. (2014) Apoplastic venom allergen-like proteins of cyst nematodes modulate the activation of basal plant innate immunity by cell surface receptors. PLOS PATH., 10: e1004569. Maxwell® 16 Instrument Meinel et. al. (2014) Next generation and unnamed Kit sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island. Genome Medicine, 6:113125. Heydt et. al. (2014) Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics. PLOS ONE, 9:e104566. Maxwell® 16 Instrument One of the Maxwell® 16 LEV simplyRNA Purification Kits Maxwell® 16 Instrument Maxwell® 16 FFPE Plus LEV DNA Purification Kit Maxwell® 16 Instrument Unidentified Maxwell® 16 FFPE DNA Purification Kit Maxwell® 16 Instrument Maxwell® 16 FFPE Plus LEV DNA Purification Kit Maxwell® 16 Instrument Maxwell® 16 FFPE Plus LEV DNA Purification Kit Hermson et. al. (2015) Genomic landscape of rat strain and substrain variation. BMC Genomics, 16:357-369. Beltran et. al. (2013) Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. Euro. Urology, 63: 920926. Javle et. al. (2013) Molecular characterization of gallbladder cancer using somatic mutation profiling. Human Pathology, 45: 701-708. Vaishnavi et. al. (2014) Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat. Med., 19: 1469-1472. Isolated RNA from brain, heart, kidney, liver, lung, muscle, ovary, skin, spleen, testis, thymus and whole blood using TRIzol® first followed by re-purification with the Maxwell® 16 Instrument and Kit. Extracted RNA from Arabidopsis using the Maxwell® 16 Instrument and one of the simplyRNA Kits and provided the RNA to BGI for RNA-seq on Illumina Instruments. Isolated gDNA from C. ulcerans using the Maxwell® Instrument and Kit followed by whole genome NGS using an Illumina MiSeq Instrument. Extracted DNA from FFPE samples using the Maxwell® 16 Instrument and FFPE Plus DNA Kit. Side-by-side comparison to other extraction methods with demonstrated the Maxwell® 16 System produced the best quality DNA which was the only DNA used in the downstream NGS using an Illumina MiSeq Instrument. Extracted DNA from FFPE samples using the Maxwell® 16 Instrument and an unidentified Maxwell® FFPE DNA Kit. Purified DNA subjected to NGS on an Illumina HiSeq 2000 Instrument. Extracted DNA from gallbladder cancer FFPE samples using the Maxwell® 16 Instrument and the FFPE Plus DNA Kit. Did target enrichment followed by NGS on an Illumina HiSeq 2000 Instrument. Extracted DNA from FFPE or frozen lung cancer samples using the Maxwell® 16 Instrument and the FFPE Plus DNA Kit. Did target enrichment followed by NGS on an Illumina HiSeq 2000 Instrument. PROMEGA CORPORATION • 2800 WOODS HOLLOW ROAD • MADISON, WI 53711-5399 USA • TELEPHONE 608-274-4330 www.promega.com • ©2015 PROMEGA CORPORATION • ALL RIGHTS RESERVED • PRICES AND SPECIFICATIONS SUBJECT TO CHANGE WITHOUT PRIOR NOTICE • CREATED 05/15

Nucleic Acid Extraction Product Used Citation Maxwell® 16 Instrument Maxwell® 16 LEV Blood DNA Kit Knudsen et. al. (2015) Revisiting bovine pyometra—New insights into the disease using a culture-independent deep sequencing approach. Vet. Micro., 175: 319-324. Maxwell® 16 Instrument Maxwell® 16 Cell LEV DNA Purification Kit Maxwell® 16 Instrument Maxwell® 16 Cell DNA Purification Kit ReliaPrep™ Blood gDNA Miniprep System De Man et. al. (2015) Draft genome sequence of a New Delhi metallo--lactamase-5 (NDM-5)-producing multidrug-resistant Escherichia coli isolate. Genome Announcements, 3: e00017-15. Kohlman...

Nucleic Acid Quantitation Before and During Library Preparation Product Used Citation Notes QuantiFluor®-ST Fluorometer QuantiFluor® dsDNA System Heydt et. al. (2014) Comparison of pre- Tested various quantitation analytical FFPE sample preparation methods/products and these two methods and their impact on massively parallel products were part of the testing. sequencing in routine diagnostics. PLOS ONE, 9:e104566. QuantiFluor® dsDNA System Van der Merwe et. al. (2014) Next-gen phyogeography of rainforest trees: Exploring landscape-level cpDNA variation from whole-genome sequencing. Mol....

Library PreparationProduct Used Citation Notes GoTaq® Green Master Mix One of the GoTaq® Master Mixes RQ1 RNase-Free DNase Wizard® SV Gel and PCR Clean-Up System Recombinant RNasin® Ribonuclease Inhibitor LigaFast™ Rapid DNA Ligation System Wizard® SV Gel and PCR Clean-Up System Wizard® SV Gel and PCR Clean-Up System Wizard® SV Gel and PCR Clean-Up System Quigley et. al. (2012) High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. App. Env. Micro., 78: 57175723. Harris et. al. (2010) Comparison of normalization methods for construction...