Ion torrent s5 xl

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Ion Torrent S5 XL is a next-generation sequencing system designed for targeted and whole-genome sequencing applications. It utilizes semiconductor-based sequencing technology to generate DNA sequence data.

Automatically generated - may contain errors

Lab products found in correlation

15 protocols using ion torrent s5 xl

Ion Torrent Ampliseq Library Prep

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA libraries were prepared according to the Ampliseq Library Preparation Kit 2.0—96Lv (Thermo Fisher, San Diego, USA, MAN0006735) standard protocol using 20 ng of input DNA, with samples barcoded using Ion Xpress Barcodes 1–96 (Thermo Fisher). Prepared libraries were diluted to 26 pM using MilliQ water and combined into four samples pools, for sequencing on four 318 chips. Twenty-five microliters of each sample pool was enriched using a One-Touch Two (OT2) machine and automated enrichment system (Thermo Fisher) with the Ion PGM^™ Template OT2 400 Kit (Thermo Fisher) to prepare Template-positive Ion Sphere Particles. Enriched products were prepared for sequencing using the Ion Personal Genome Machine^™ (PGM) Hi-Q Sequencing Kit and run on the Personal Genome Machine using the Ion 318 chip v2 (Thermo Fisher, MAN0009816). In parallel, libraries for each sample were diluted to 70 pM and loaded onto an Ion Chef for sequencing on an Ion Torrent S5 XL^™ using an Ion 530 chip (Thermo Fisher, MAN0010851) (Fig 1).

Bailie C., Kilner J., Maxwell A.P, & McKnight A.J. (2017). Development of next generation sequencing panel for UMOD and association with kidney disease. PLoS ONE, 12(6), e0178321.

+ Open protocol

+ Expand

Avian RT-PCR Amplicon Sequencing

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

The purified avian RT-PCR amplicons were sequenced on the IonTorrent platform (Thermo Fisher Scientific) as previously described [5 (link), 10 (link)]. Before library preparation for the respective platform, the samples were mechanically fragmented to a 500 bp size on a Covaris M220 Ultrasonicator (Covaris Ltd., Brighton, UK). The GeneRead DNA L Core Kit (Qiagen) was subsequently used for library preparation with Xpress Barcode Adapters (Qiagen). After a following size selection and clean-up step with AMPure XP Beads (Beckman Coulter), the final library was quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Böblingen, Germany) and quantized via qPCR with the KAPA Library Quantification Kit (Roche, Mannheim, Germany). Sequencing was conducted on the IonTorrent S5XL (Thermo Fisher Scientific) in combination with the Ion OneTouch 2 System (Thermo Fisher Scientific), encompassing twelve AIV samples per Ion 530 Chip (Thermo Fisher Scientific).

King J., Harder T., Beer M, & Pohlmann A. (2020). Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses. BMC Infectious Diseases, 20, 648.

+ Open protocol

+ Expand

Whole-Genome Sequencing of STEC Strains

Cited 3 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA extracted from the two Swedish STEC strains was analyzed using the Ion Torrent S5 XL platform (Thermo Fisher Scientific, Waltham, Massachusetts, USA) as previously described [11 (link)]. The sequencing reads were de novo assembled with Spades (v3.13.1) [12 (link)] in “careful mode” to correct mismatches. The Danish strain was sequenced using an Illumina Nextseq (Illumina, San Diego, CA, USA) as previously described [13 (link)]. The sequencing reads were de novo assembled with SKESA (version 2.3.0) with default settings [14 (link)].

Bai X., Scheutz F., Dahlgren H.M., Hedenström I, & Jernberg C. (2021). Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark. Microorganisms, 9(11), 2374.

+ Open protocol

+ Expand

RNA-seq from patient 343VY

Check if the same lab product or an alternative is used in the 5 most similar protocols

Samples for RNA-seq from patient 343VY were prepared as previously described [13 ]. Briefly, cells were harvested by LMD into Buffer RLT with β-mercaptoethanol and RNA isolated using the RNeasy Micro Kit (Qiagen) per the manufacturer’s instructions. RNA concentrations were determined by fluorescence (Qubit HS and BR kits, ThermoFisher Scientific, Inc.). RNA integrity numbers (RIN) were determined using the RNA 6000 Pico Kit 2100 Bioanalyzer (Agilent Technologies, Inc.); RIN values were > 6 for all levels and collection types. RNA samples were reverse transcribed to generate barcoded cDNA libraries that were sequenced on the Ion Torrent S5 XL (ThermoFisher Scientific, Inc.). Barcoded cDNA libraries contained 6 LMD RNA samples, a Universal Human Reference RNA (UHR) standard (Stratagene), and a no-template control (NTC) water blank. Successful sequencing runs achieved an average of 18 M reads/sample (with one exception) and 167-205X AQ20 mean coverage depth.

Hunt A.L., Bateman N.W., Barakat W., Makohon-Moore S.C., Abulez T., Driscoll J.A., Schaaf J.P., Hood B.L., Conrads K.A., Zhou M., Calvert V., Pierobon M., Loffredo J., Wilson K.N., Litzi T.J., Teng P.N., Oliver J., Mitchell D., Gist G., Rojas C., Blanton B., Darcy K.M., Rao U.N., Petricoin E.F., Phippen N.T., Maxwell G.L, & Conrads T.P. (2024). Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling. Clinical Proteomics, 21, 4.

+ Open protocol

+ Expand

Molecular profiling of B-cell lymphomas

Check if the same lab product or an alternative is used in the 5 most similar protocols

Tumor specimens for molecular analysis were available for 72 patients. As detailed elsewhere [36 (link)], somatic mutations were detected by targeted high-throughput sequencing (HTS) using a target enrichment panel covering either mutational hotspots or all exons of 68 genes most frequently mutated in B-cell lymphomas. Sequencing was performed by the Ion Torrent S5 XL machine (Thermo Fisher Scientific, Carlsbad, CA, USA).

Genta S., Ghilardi G., Cascione L., Juskevicius D., Tzankov A., Schär S., Milan L., Pirosa M.C., Esposito F., Ruberto T., Giovanella L., Hayoz S., Mamot C., Dirnhofer S., Zucca E, & Ceriani L. (2022). Integration of Baseline Metabolic Parameters and Mutational Profiles Predicts Long-Term Response to First-Line Therapy in DLBCL Patients: A Post Hoc Analysis of the SAKK38/07 Study. Cancers, 14(4), 1018.

+ Open protocol

+ Expand

Targeted NGS of FFPE Tumor Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols

Targeted next-generation sequencing (NGS) was performed using formalin-fixed paraffin-embedded (FFPE) tumor tissue. Hematoxylin and eosin (H&E)-stained slides were reviewed, and the tumor area with enough viable tumor cells was marked and used as a guide for macrodissection. Areas with greater than 50% tumor volume were used for examination. In brief, total nucleic acid was isolated from FFPE tumor tissue using a RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Ambion, Austin, TX, USA), according to the manufacturer’s specifications. The samples were analyzed using the Oncomine Comprehensive Assay Cancer Panel (Ion Torrent S5 XL, Thermo Fisher Scientific, MA, USA) which covers 2,737 amplicons (2530 DNA + 207 RNA) within 143 cancer-related genes. The percentage of amplicons covered was 95%. Reads were aligned to the hg19 reference genome, and variants with allele frequencies less than 3% were excluded. The Oncomine Comprehensive Assay Cancer Panel included 15 amplicons located in PIK3CA exons 1, 2, 3, 4, 6, 7, 9, 13, 18, 19, and 20.

Ahn A.R., Kim K.M., Jang K.Y., Moon W.S., Ha G.W., Lee M.R, & Chung M.J. (2021). Correlation of PIK3CA mutation with programmed death ligand-1 (PD-L1) expression and their clinicopathological significance in colorectal cancer. Annals of Translational Medicine, 9(18), 1406.

+ Open protocol

+ Expand

FFPE Tumor Sequencing Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

The nucleic acids were extracted with the Maxwell RSC DNA FFPE kit (Promega, Madison, WI, USA) from formalin-fixed, paraffin-embedded (FFPE) tumor samples. For amplification screening, we used our custom panel Oncomine Solid Tumor and Oncomine Solid Tumor+ (OST/OST+), which includes EGFR. For all clinical samples, we performed sequencing with Ion Torrent S5XL (ThermoFisher Scientifics, Waltham, MA, USA) with a sensitivity of 5% and a minimum coverage of 500×. Then, data were analyzed through two complementary pipelines. The first pipeline was developed by ThermoFisher on the IonTorrent Suite + Ion Reporter. The second pipeline, which was developed in our laboratory, uses open-source software such as BWA-MEM for alignment, SAMtools for mpileup, VarScan2 as the variant caller and VEP Ensemble for annotations.

Eyraud R., Ayache S., Tsvetkov P.O., Kalidindi S.S., Baksheeva V.E., Boissonneau S., Jiguet-Jiglaire C., Appay R., Nanni-Metellus I., Chinot O., Devred F, & Tabouret E. (2023). Plasma nanoDSF Denaturation Profile at Baseline Is Predictive of Glioblastoma EGFR Status. Cancers, 15(3), 760.

+ Open protocol

+ Expand

Liquid Biopsy in NSCLC Patients

Check if the same lab product or an alternative is used in the 5 most similar protocols

During April 2017 and August 2017, peripheral whole blood was collected from 12 non-small cell lung cancer patients during ongoing treatment, five before initiation of first line systemic therapy (Samples P2-P5), one after post-surgery (P1) and six patients after first line systemic therapy (S1-S6). All patients harboured an activating mutation either in the EGFR or KRAS gene (Table 1). The activating mutation had already been analysed from FFPE tissue during routine diagnostics prior to blood sampling using targeted sequencing with the AmpliSeq Colon Lung Panel v2 on the Ion Torrent S5XL instrument (Thermo Scientific, Waltham, USA). Only Sample S5 was analyzed by pyrosequencing as NGS was not practiced in our institute at the time point of first diagnosis in 2010 and no more tissue or DNA was left to retest the latter with NGS methods.
Informed consent was obtained from each patient with protocols approved by an ethical committee.

Streubel A., Stenzinger A., Stephan-Falkenau S., Kollmeier J., Misch D., Blum T.G., Bauer T., Landt O., Am Ende A., Schirmacher P., Mairinger T, & Endris V. (2019). Comparison of different semi-automated cfDNA extraction methods in combination with UMI-based targeted sequencing. Oncotarget, 10(55), 5690-5702.

+ Open protocol

+ Expand

Ion Torrent RNA Sequencing Library Prep

Check if the same lab product or an alternative is used in the 5 most similar protocols

Ion Torrent Libraries were generated using the Ion AmpliSeq Library Kit 2.0 (Thermo Fisher, Waltham, MA) according to manufacturer's instructions using 10 ng input material. RNA was first reverse transcribed with SuperScript IV VILO (Thermo Fisher, Waltham, MA). Following cleanup, libraries were quantitated using qPCR on a QuantStudio 6 (Thermo Fisher, Waltham, MA), normalized to 100 pM, and loaded onto the IonChef (Thermo Fisher, Waltham, MA). Pooled libraries were loaded onto the Ion 540 Chip (Thermo Fisher, Waltham, MA) and sequenced on the Ion Torrent S5XL (Thermo Fisher, Waltham, MA).

Angell T.E., Wirth L.J., Cabanillas M.E., Shindo M.L., Cibas E.S., Babiarz J.E., Hao Y., Kim S.Y., Walsh P.S., Huang J., Kloos R.T., Kennedy G.C, & Waguespack S.G. (2019). Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples. Frontiers in Endocrinology, 10, 612.

+ Open protocol

+ Expand

Multimodal Profiling of Tumor Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA and RNA were co-extracted from each sample and processed for gene expression by RNA-seq and TMB by DNA-seq, as previously described [9 (link)]. Nucleic acids were quantitated by Qubit fluorometer (Thermo Fisher Scientific) using ribogreen staining for RNA and picogreen staining for DNA. Gene expression were evaluated by RNA sequencing of 395 transcripts on samples that met validated quality control (QC) thresholds [9 (link)]. TMB was measured by DNA sequencing of the full coding region of 409 cancer related genes as non-synonymous mutations per megabase (Mut/Mb) of sequenced DNA on samples with > 30% tumor nuclei. RNA and DNA libraries were sequenced to appropriate depth on the Ion Torrent S5XL sequencer (Thermo Fisher Scientific).

Pabla S., Seager R.J., Van Roey E., Gao S., Hoefer C., Nesline M.K., DePietro P., Burgher B., Andreas J., Giamo V., Wang Y., Lenzo F.L., Schoenborn M., Zhang S., Klein R., Glenn S.T, & Conroy J.M. (2021). Integration of tumor inflammation, cell proliferation, and traditional biomarkers improves prediction of immunotherapy resistance and response. Biomarker Research, 9, 56.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!