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Ion onetouch 200 template kit v2 dl

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The Ion OneTouch 200 Template Kit v2 DL is a laboratory equipment product designed for sample preparation. It is used to generate template-positive Ion Sphere Particles for sequencing on Ion Torrent systems.

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Lab products found in correlation

Ion pgm 200 sequencing kit, by Thermo Fisher Scientific (5 mentions) Ion onetouch es, by Thermo Fisher Scientific (4 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions) Ampure bead, by Beckman Coulter (2 mentions) Ion sequencing 200 kit, by Thermo Fisher Scientific (2 mentions) Ion torrent pgm system, by Thermo Fisher Scientific (2 mentions) Ion xpress plus fragment library kit, by Thermo Fisher Scientific (2 mentions) Ion pgm sequencing 200 kit v2, by Thermo Fisher Scientific (2 mentions) Ion torrent pgm, by Thermo Fisher Scientific (2 mentions) Ion sphere quality control kit, by Thermo Fisher Scientific (2 mentions) Ion xpress barcode adapters 1 16 kit, by Thermo Fisher Scientific (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Ion 318 chip, by Thermo Fisher Scientific (2 mentions) Total exosome rna and protein isolation kit, by Thermo Fisher Scientific (1 mentions) Ion total rnaseq v2 kit, by Thermo Fisher Scientific (1 mentions) Ion plus fragment library kit, by Thermo Fisher Scientific (1 mentions) Wizard sv gen pcr clean up system, by Promega (1 mentions) Ampure xp dna purification beads, by Beckman Coulter (1 mentions) Ion torrent pgm sequencer, by Thermo Fisher Scientific (1 mentions) Ion sequencing 200 kit v2, by Thermo Fisher Scientific (1 mentions)

18 protocols using ion onetouch 200 template kit v2 dl

1

Exosomal RNA Extraction and Sequencing

Cited 2 times
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As reported previously [11 (link)], RNA extraction was performed using the Total Exosome RNA and Protein Isolation Kit (catalog # 4478545; Invitrogen, USA) according to the provided instructions. 200 ng-1 μg RNA in final volume of 30 μL solution was collected for each sample. Total RNA quantity and quality (260/280 absorbance ratio) were assessed using NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) and Agilent 2100 Bioanalyzer to test concentration and inorganic ions or polycarbonate contamination. miRNA sequence was isolated by BGI Company (China) based on previous instructions [12 (link)]. cDNA libraries were constructed using the Ion Total RNA-Seqv2 kit (Life Technologies, USA) (n = 3 for each group) and purified using AMPure beads (Beckman Coulter). Emulsion PCR and enrichment of cDNA-conjugated particles were performed with an Ion OneTouch 200 Template Kit v2 DL (Life Technologies). The final cDNA samples were sequenced single end on the HiSeq 2000 System with a 50 bp read length.
Mao K, & Wu X. (2020). Microarray Analysis of Small Extracellular Vesicle-Derived miRNAs Involved in Oxidative Stress of RPE Cells. Oxidative Medicine and Cellular Longevity, 2020, 7658921.
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2

Ion Torrent PGM Whole Genome Sequencing

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Whole genome library was performed using Ionplus fragment library kit (Life Technologies, Carlsbad, CA, USA). Emulsion PCR was carried out using the IonOnetouch 200 Template kit v2 DL (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. Sequencing of the libraries was carried out on a 318 chip using the Ion Torrent PGM system and Ion Sequencing 200kit (Life Technologies, Carlsbad, CA, USA).
Dsouza R., Pinto N.A., Hwang I., Cho Y., Yong D., Choi J., Lee K, & Chong Y. (2017). Panel strain of Klebsiella pneumoniae for beta-lactam antibiotic evaluation: their phenotypic and genotypic characterization. PeerJ, 5, e2896.
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3

Genome Sequencing and Deletion Analysis

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RB733 genomic DNA was purified by phenol and chloroform extraction including
RNase A treatment. 1 μg DNA was subjected to
fragmentation and adaptor ligation using an Ion Xpress Plus Fragment Library Kit
(Life Technologies), according to the manufacturer’s instructions.
The library was subjected to emulsion PCR using the Ion OneTouch 200 Template
Kit v2 DL (Life Technologies), followed by bead enrichment. Then, whole-genome
sequencing was performed with an Ion Torrent PGM system using the Ion PGM 200
Sequencing Kit and Ion 318 chip (Life Technologies). Using IGV (Integrative
Genomics Viewer), we inspected the genome region where no read was aligned as
the potential deletion candidates. Except for ok498, we found two
potential deletions larger than 1 kb on chromosome X. One of the two
genomic regions contains no protein-coding gene, thus we focused on another
region, around chromosome X: +6.73 cM. This mutation candidate was
confirmed by Sanger sequencing and revealed a 7809 bp deletion and
7 bp insertion located in the genomic region of rsd-3.
Imae R., Dejima K., Kage-Nakadai E., Arai H, & Mitani S. (2016). Endomembrane-associated RSD-3 is important for RNAi induced by extracellular silencing RNA in both somatic and germ cells of Caenorhabditis elegans. Scientific Reports, 6, 28198.
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4

Amplicon Sequencing Library Preparation

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Primer selection, amplicon generation and purification, amplicon library construction and sequencing were performed essentially as described by Hevia et al. [17 (link)]. Briefly, the primer pair Probio_Uni / Probio_Rev [16 (link)] was used to generate amplicon pools of approximately 200 bp length. The integrity of the PCR amplicons was analyzed by electrophoresis prior to their purification using the Wizard SV Gen PCR Clean-Up System (Promega, Madison, WI), and the Agencourt AMPure XP DNA purification beads (Beckman Coulter Genomics GmbH, Bernried, Germany). Libraries for each run were diluted to 3E9 DNA molecules prior to clonal amplification. Emulsion PCR was carried out using the Ion OneTouch™ 200 Template Kit v2 DL (Life Technologies, Guilford, CA) and sequencing of the amplicon libraries was carried out on 316 chips using the Ion Torrent PGM system and employing the Ion Sequencing 200 kit (Life Technologies). After sequencing, individual sequence reads were filtered by the PGM software to remove low quality and polyclonal sequences. Sequences matching the PGM 3’ adaptor were also automatically trimmed. All PGM quality-approved, trimmed and filtered data were exported as SFF files.
Hevia A., Milani C., López P., Donado C.D., Cuervo A., González S., Suárez A., Turroni F., Gueimonde M., Ventura M., Sánchez B, & Margolles A. (2016). Allergic Patients with Long-Term Asthma Display Low Levels of Bifidobacterium adolescentis. PLoS ONE, 11(2), e0147809.
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5

Ion Torrent Sequencing of PCR Products

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The libraries were prepared using 50 ng of the PCR products with DNA NEBNext Fast DNA Library Prep Set for Ion Torrent (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s protocol, and sequenced with the Ion Torrent PGM sequencer (Life Technologies) at 100x coverage using the Ion OneTouch 200 Template Kit v2 DL and the Ion PGM Sequencing 200 Kit v2 with the 314 or 316 chip kits (all produced by Life Technologies), following the manufacturer’s instructions. The data analysis was conducted using Geneious version 6.0.1 (http://www.geneious.com) (Kearse et al., 2012 ).
Gheit T., Dutta S., Oliver J., Robitaille A., Hampras S., Combes J.D., McKay-Chopin S., Le Calvez-Kelm F., Fenske N., Cherpelis B., Giuliano A.R., Franceschi S., McKay J., Rollison D.E, & Tommasino M. (2017). Isolation and characterization of a novel putative human polyomavirus. Virology, 506, 45-54.
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6

Ion Torrent Sequencing Protocol

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Emulsion PCR was performed using the Ion OneTouch 200 Template Kit v2 DL (catalog No. MAN0006957; Life Technologies, USA). Sequencing of the amplicon libraries was performed on a 314 chip with the Ion Torrent personal genome machine system using the Ion Sequencing 200 kit v2 (catalog No. MAN0007273; Life Technologies, USA).
Zhao L., Meng Q., Ren L., Liu W., Zhang X., Huo Y, & Zhou Z. (2015). Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance. Asian-Australasian Journal of Animal Sciences, 28(10), 1433-1441.
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7

Teleaulax amphioxeia Genome Sequencing

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A culture derived from a single-cell isolate of Teleaulax amphioxeia collected from Gomso Bay, Korea (35° 40’ N, 126° 40’ E), which was established in a previous study [56 ], was selected for genome sequencing. DNA was extracted from the cultivated sample using a QIAGEN DNEasy Blood Mini Kit (QIAGEN, Valencia, CA, USA), following the manufacturer’s instructions. A sequencing library was prepared using an Ion Xpress Plus gDNA Fragment Library Preparation Kit and an Ion OneTouch 200 Template Kit v2 DL (Life Technologies, San Francisco, CA, USA) according to the manufacturer’s protocol and sequenced with an Ion Torrent Personal Genome Machine (PGM) at the Yoon laboratory at Sungkyunkwan University (Suwon, Korea) using an Ion PGM Sequencing 200 Kit v2 (Life Technologies, San Francisco, CA, USA).
Kim J.I., Yoon H.S., Yi G., Kim H.S., Yih W, & Shin W. (2015). The Plastid Genome of the Cryptomonad Teleaulax amphioxeia. PLoS ONE, 10(6), e0129284.
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8

NGS-based Cancer Hotspot Panel Profiling

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The NGS was conducted by using the Ion AmpliSeq Cancer Hotspot Panel (v2) for targeted multigene amplification (207 amplicons covering approximately 2,800 Catalog of Somatic Mutations in Cancer [COSMIC, http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/; last accessed May 1, 2013]) mutations from 50 oncogenes and tumor suppressor genes), Ion AmpliSeq Library Kit 2.0 for library preparation, Ion OneTouch 200 Template Kit v2 DL and Ion OneTouch ES Instrument for emulsion PCR and enrichment, Ion PGM 200 Sequencing Kit, Ion 318 Chips, and the PGM sequencing platform for massive parallel sequencing (Life Technologies), as recommended by the manufacturers’ protocols without modification. The DNA input for targeted multigene PCR was 10 to 30 ng. Eight specimens were barcoded using Ion Xpress Barcode Adapters (Life Technologies), pooled, and run on a single Ion 318 chip. We attempted a parallel validation using the TruSeq panel but were unable to complete it due to the requirement of 250 ng of input DNA, which we were unable to obtain for most solid tumors.
Lin M.T., Mosier S.L., Thiess M., Beierl K.F., Debeljak M., Tseng L.H., Chen G., Yegnasubramanian S., Ho H., Cope L., Wheelan S.J., Gocke C.D, & Eshleman J.R. (2014). Clinical Validation of KRAS, BRAF, and EGFR Mutation Detection Using Next-Generation Sequencing. American journal of clinical pathology, 141(6), 856-866.
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9

16S rRNA Sequencing of Vaginal Microbiome

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cDNA amplification and Ion Torrent PGM sequencing of 16S rRNA gene-based amplicons were performed by GENPROBIO srl (Parma, Italy). cDNA obtained from vaginal swab specimens at times T0, T1, and T2 was amplified using the primer pair Probio_Uni /Probio_Rev, which targets the V3 region of the 16S rRNA gene sequence [36]. DNA was amplified under the polymerase chain reaction (PCR) conditions described previously [37]. PCR amplicons were analyzed by electrophoresis on an Experion workstation (Bio-Rad, UK) and quantified using the Experion system (Bio-Rad, UK). Emulsion PCR was performed using the Ion OneTouch™ 200 Template Kit v2 DL (Life Technologies, San Francisco, CA, USA) according to the manufacturer’s instructions. Sequencing analysis was carried out according to the protocol of the Ion Torrent PGM system and using the Ion Sequencing 200 kit. Sequence reads were analyzed by PGM software to delete low-quality and polyclonal sequences. High-quality sequences were trimmed and filtered with the default settings, using QIIME pipeline version 1.4.0 (http://qiime.sourceforge.net). Filtered sequences were exported as sff files.
Pino A., Giunta G., Randazzo C.L., Caruso S., Caggia C, & Cianci A. (2017). Bacterial biota of women with bacterial vaginosis treated with lactoferrin: an open prospective randomized trial. Microbial Ecology in Health and Disease, 28(1), 1357417.
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10

Targeted Genetic Screening for Disease-Causing Variants

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Fifteen bar-coded samples were pooled in equimolar amounts. Amplified libraries were submitted to emulsion polymerase chain reaction done on the Ion OneTouch system using the Ion OneTouch 200 Template Kit v2 DL (Life Technologies; Thermo Fisher Scientific), according to the manufacturer’s instructions. Next, ion sphere particles were recovered, and template-positive ion sphere particles were enriched using the Ion OneTouch ES system (Life Technologies; Thermo Fisher Scientific). The enriched ion sphere particles were sequenced on an Ion 318 chip using the Ion PGM 200 Sequencing Kit (Life Technologies; Thermo Fisher Scientific) on the Ion Torrent PGM (Life Technologies; Thermo Fisher Scientific). Data from the PGM runs were processed using Ion Torrent Suite 4.0 software (Life Technologies; Thermo Fisher Scientific) to generate sequence reads. After sequence alignment and extraction of SNPs and indels, all variants were filtered against dbSNP137. DNA sequences were visualized with an integrated genomics viewer. The most likely disease-causing variants were analyzed by Sanger sequencing.
This study, including both clinical evaluation and broad targeted genetic screening, was approved by the Peking Union Medical College Hospital ethics committee. Written informed consent forms were obtained from all investigated participants.
Wu W., Lu C.X., Wang Y.N., Liu F., Chen W., Liu Y.T., Han Y.C., Cao J., Zhang S.Y, & Zhang X. (2015). Novel Phenotype–Genotype Correlations of Restrictive Cardiomyopathy With Myosin-Binding Protein C (MYBPC3) Gene Mutations Tested by Next-Generation Sequencing. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 4(7), e001879.
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