Lsk 109 sequencing kit

Manufactured by Oxford Nanopore

Sourced in United Kingdom

The LSK-109 sequencing kit is a laboratory product offered by Oxford Nanopore. It is designed for DNA/RNA sequencing applications. The kit contains the necessary reagents and consumables required to perform sequencing experiments using Oxford Nanopore's technology.

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Lab products found in correlation

Nextseq 550, by Illumina (1 mentions) Nextera xt kit, by Illumina (1 mentions) Clc genomics workbench version 20, by Qiagen (1 mentions) Gridion instrument, by Oxford Nanopore (1 mentions)

2 protocols using lsk 109 sequencing kit

SARS-CoV-2 Whole-Genome Sequencing Protocol

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Libraries for whole viral genome sequencing were prepared according to version 1 ARTIC nCoV-2019 sequencing protocol (https://artic.network/ncov-2019, last accessed May 6, 2020). Long reads were generated with the LSK-109 sequencing kit, 24 native barcodes (NBD104 and NBD114 kits), and a GridION instrument (Oxford Nanopore, Oxford, UK). Short reads were generated with the NexteraXT kit and a MiSeq or NextSeq 550 instrument (Illumina, San Diego, CA). Whole genome alignments of consensus viral genome sequence generated from the ARTIC nCoV-2019 bioinformatics pipeline were trimmed to the start of orf1ab and the end of orf10 and used to generate a phylogenetic tree using RAxML version 8.2 (https://cme.h-its.org/exelixis/web/software/raxml/index.html, last accessed May 3, 2020)²⁶ to determine viral clade. Trees were visualized and annotated with CLC Genomics Workbench version 20 (Qiagen).

Salazar E., Perez K.K., Ashraf M., Chen J., Castillo B., Christensen P.A., Eubank T., Bernard D.W., Eagar T.N., Long S.W., Subedi S., Olsen R.J., Leveque C., Schwartz M.R., Dey M., Chavez-East C., Rogers J., Shehabeldin A., Joseph D., Williams G., Thomas K., Masud F., Talley C., Dlouhy K.G., Lopez B.V., Hampton C., Lavinder J., Gollihar J.D., Maranhao A.C., Ippolito G.C., Saavedra M.O., Cantu C.C., Yerramilli P., Pruitt L, & Musser J.M. (2020). Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma. The American Journal of Pathology, 190(8), 1680-1690.

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Nanopore Sequencing of Genomic DNA

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Oxford Nanopore Technologies (ONT) sequencing libraries were prepared from genomic DNA using the LSK-109 sequencing kit with minor modifications. Namely, end-repair, A-tailing, and ligation incubation times were increased to 30 min each. Libraries were sequenced on the ONT MinION using a R9.4.1 flow cell. Fast5 raw data files were basecalled and converted into FASTQ files using the ONT research basecaller flappie [Version 1.0.0] (https://github.com/nanoporetech/flappie).

Escalona M., VanCampen J., Maurer N.W., Haukness M., Okhovat M., Harris R.S., Watwood A., Hartley G.A., O’Neill R.J., Medvedev P., Makova K.D., Vollmers C., Carbone L, & Green R.E. (2022). Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). Journal of Heredity, 114(1), 35-43.

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