Ion 318 chip kit v2 bc

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Ion 318 Chip Kit v2 BC is a consumable product designed for use with Ion Torrent sequencing platforms. The kit contains materials necessary for the preparation and loading of DNA samples onto the Ion 318 sequencing chip, which is used to perform next-generation DNA sequencing.

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Ion 318 Chip (61 citations) ChIP kit (45 citations) 318 chip (13 citations) 318 Chip v2 (2 citations)

4 protocols using ion 318 chip kit v2 bc

Targeted FH-Related Gene Sequencing

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NGS was conducted using samples from the proband’s first-degree blood relatives [mother (I.2), brother (II.1), sister (II.2), and daughter (III.1)]. Following the manufacturer’s guidelines, the QIAamp DNA Blood Mini Kit (Qiagen) was used to extract genomic DNA from EDTA-treated whole blood. The NanoDrop 2000 instrument was used to determine the quantity and purity of extracted DNA (Thermo Fisher Scientific, Waltham, MA, USA). We created an Ion AmpliSeq panel with exons and surrounding intron regions from four FH-related genes (LDLR, APOB, PCSK9, and LDLRAP1). To prepare the library for sequencing on the Ion Chef System, the tailored Ion AmpliSeq panel primers pools and Ion AmpliSeq Kit for Chef DL8 were used (Thermo Fisher Scientific, Waltham, MA, USA). The Ion Chef system was used to prepare emulsion PCR-based templates and load chips, with the Ion PGM Hi-Q View Chef Kit and the Ion 318 Chip Kit v2 BC (Thermo Fisher Scientific, Waltham, MA, USA). Finally, the Ion PGM sequencer was used to conduct the sequencing (Thermo Fisher Scientific, Waltham, MA, USA).

Athar M., Toonsi M., Abduljaleel Z., Bouazzaoui A., Bogari N.M., Dannoun A, & Al-Allaf F.A. (2023). Novel LDLR Variant in Familial Hypercholesterolemia: NGS-Based Identification, In Silico Characterization, and Pharmacogenetic Insights. Life, 13(7), 1542.

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Ion AmpliSeq Targeted Sequencing

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Barcoded libraries were generated from 20 ng of DNA per sample using the Ion AmpliSeq HiFi mix (Ion AmpliSeq Library Kit Plus, Thermo Fisher Scientific) and two premixed pools of 952 primer pairs (Thermo Fisher Scientific), according to the manufacturer’s instructions. The clonal amplification of the libraries was performed by emulsion PCR on an Ion OneTouch™ 2 System. Sequencing was performed on the Ion Personal Genome Machine™ (PGM™) System using an Ion 318™ Chip Kit v2 BC and the Ion PGM™ Hi-Q™ View Sequencing Kit (all Thermo Fisher Scientific). Alignments were visualized with a Tablet v1.21.02.08 (https://ics.hutton.ac.uk/tablet/, accessed on 8 February 2021).

Domenis R., Cifù A., Mio C., Fabris M, & Curcio F. (2021). Pro-Inflammatory Microenvironment Modulates the Transfer of Mutated TP53 Mediated by Tumor Exosomes. International Journal of Molecular Sciences, 22(12), 6258.

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Amplicon Sequencing of HTLV-1 LTR Regions

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The semi-nested PCR products were purified using Agencourt AMPure XP (Beckman Coulter) according to the manufacturer’s instructions. The purified amplicons were quantified using a Bioanalyzer High Sensitivity DNA Analysis (Agilent) system, diluted with water to 18 pM, and mixed with Ion PGM Hi-Q View Ion Sphere Particles (ISPs) using an Ion PGM Hi-Q View OT2 Kit (Thermo Fisher Scientific) in the Ion OneTouch 2 System (Thermo Fisher Scientific). The template-positive Ion PGM Hi-Q View ISPs were prepared according to the Ion PGM Hi-Q View OT2 Kit - 400 protocol and sequenced using an Ion PGM Hi-Q View Sequencing Kit (Thermo Fisher Scientific) and Ion 318 Chip Kit v2 BC (Thermo Fisher Scientific). Sequencing data were analyzed using CLC Genomics Workbench (CLC Bio). The HTLV-1 3′ LTR and the adaptor sequence were trimmed from the amplicon sequence and UISs were clustered by operational taxonomical unit (OTU) clustering analysis and the UISs of dominant clones were identified. The amplicons generated from the HTLV-1 5′ LTR that contained only viral sequences were removed before clustering analysis.

Yamakawa T., Uno N., Sasaki D., Kaku N., Sakamoto K., Kosai K., Hasegawa H., Miyazaki Y, & Yanagihara K. (2020). A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma. Molecular Therapy. Methods & Clinical Development, 19, 467-473.

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Anammox Cells DNA Extraction Protocol

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For DNA extraction from the anammox cells, approximately 100 mg of the gel carrier was homogenized in microtubes. The total DNA was extracted using the ISOPLANT kit (Nippon Gene Inc., Toyama, Japan). The V7–V8 hypervariable regions of the 16S rRNA gene were amplified using 1055F/1392R primers (Ferris et al., 1996 (link)) and Ion Xpress Barcode Adaptor sequences. The amplicon samples obtained through the polymerase chain reaction were purified on E-Gel SizeSelect II agarose gels (Thermo Fisher Scientific, Waltham, MA, United States). Following the manufacturer’s instructions, a template sample was prepared using the Ion OneTouch 2 system (Thermo Fisher Scientific, Waltham, MA, United States) and an Ion PGM Hi-Q View OT2 kit (Thermo Fisher Scientific, Waltham, MA, United States). Sequencing was performed on an Ion Torrent PGM system (Thermo Fisher Scientific) using an Ion PGM Hi-Q View sequencing kit and an Ion 318 Chip kit v2 BC (Thermo Fisher Scientific). The readings of the sequencing were trimmed to remove the adaptor and barcode sequences. High-quality filtering was performed on a CLC genomics workbench (Qiagen, Aarhus, Germany), setting a minimum quality score of 0.05 and a sequencing length of 300–400 bp. The obtained sequence data were processed using QIIME 1.7.0 (Caporaso et al., 2010 (link)).

Isaka K., Sugawara D., Yamazaki H., Kimura Y., Osaka T, & Tsuneda S. (2022). Long-Term Limitation Effects of Se(VI), Zn(II), and Ni(II) on Start-Up of the Anammox Process Using Gel Carrier. Frontiers in Bioengineering and Biotechnology, 10, 851617.

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