Ion pi template ot2 200 kit v3

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Ion PI Template OT2 200 Kit v3 is a laboratory equipment product designed for preparing Ion Torrent sequencing templates. It includes reagents and consumables necessary for the template preparation workflow using the Ion OneTouch 2 System. The kit provides the tools to generate high-quality sequencing templates from DNA or RNA samples.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

Ion PI OT2 200 Kit (3 citations) Ion PITM Template OT2 200 Kit v3 (2 citations)

25 protocols using ion pi template ot2 200 kit v3

Sequencing-Based Fusion Detection

Cited 1 time

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

DNA and RNA were co-isolated from each specimen as previously described.(23 ) DNA and RNA libraries were generated per sample using the Ion Ampliseq Library kit (Life Technologies, Foster City, CA), as described.(23 ) We prepared templates for DNA and RNA libraries using the Ion PI Template OT2 200 Kit v3 on the Ion One Touch 2 and sequencing was performed on Ion Proton P1 chips using the Ion PI Sequencing 200 Kit v3 (200 base pair reads), essentially as described.(24 (link),25 ) NGS data analysis was performed using Torrent Suite (4.2.0) and the Coverage Analysis Plug-ins (both v4.0-r73765), along with the Ion Reporter (4.2.0) Targeted NGS, fusion analysis workflow and in house validated pipelines as described in the Supplementary Methods.(24 (link)-27 ) A sample was classified as fusion positive if a fusion isoform was supported by ≥ 20 reads and ≥ 3.0% total mapped reads, otherwise is classified as fusion negative.

Palapattu G.S., Salami S.S., Cani A.K., Hovelson D.H., de la Vega L.L., Vandenberg K.R., Bratley J.V., Liu C.J., Kunju L.P., Montgomery J.S., Morgan T.M., Natarajan S., Huang J., Tomlins S.A, & Marks L.S. (2016). Molecular Profiling to Determine Clonality of Serial Magnetic Resonance Imaging/Ultrasound Fusion Biopsies from Men on Active Surveillance for Low Risk Prostate Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 23(4), 985-991.

+ Open protocol

+ Expand

High-throughput RNA-seq Protocol

Cited 2 times

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

RNA-seq was performed as described previously.^{45 (link)} cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies). High-throughput sequencing of the cDNA fragments was performed using Ion PROTON, Ion PI Template OT2 200 Kit v.3 and Ion PI Sequencing 200 Kit v.3 or Ion PI IC 200 Kit (Life Technologies) following the manufacturer's protocols. P1 chip v.2 (Life Technologies) was used to sequence three pooled barcoded samples. Sequence reads, whose individual read lengths were determined by evaluating the default sequencing quality using the Torrent Server (Life Technologies), were aligned against the human reference transcriptome (NCBI Build 37, hg19) in TopHat2 (http://ccb.jhu.edu/software/tophat/index.shtml).^{46 (link)} Expression levels were calculated by using the cuffdiff function of Cufflinks (http://cufflinks.cbcb.umd.edu/). Raw sequencing data with FPKM (fragments per kilobase of exon per million mapped sequence reads) calculation results are available at GEO (GSE66741 and GSE60559).

Mizutani A., Koinuma D., Seimiya H, & Miyazono K. (2015). The Arkadia-ESRP2 axis suppresses tumor progression: analyses in clear-cell renal cell carcinoma. Oncogene, 35(27), 3514-3523.

+ Open protocol

+ Expand

EV-miRNA Profiling in Cancer Serum

Cited 2 times

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

Characterization and quantification of the EV-miRNA profile from serum samples of patients and controls were performed by RNA-seq. The Libraries were constructed using the Ion total RNA-seq kit v2 for Whole Transcriptome Library (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s instructions for small RNA libraries. Six pools (CT1, CT2, LA1, LA2, TNBC1, and TNBC2) were sequenced on the Next Generation sequencing platform Ion Proton™ System^® (Thermo Fisher Scientific, MA, USA) platform using the Ion PI Template OT2 200 Kit v3 and the Ion PI Sequencing 200 Kit v3 (Life Technologies) following the manufacturer’s instructions. Data alignment and mapping were performed with the MiRMaster platform (www.ccb.uni-saarland.de/mirmaster) [22 (link)]. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using Diana Tools mirPath v.3 online, selected for the Tarbase database [23 (link)]. Cancer group (CA) was defined by the combined analysis of the LA and TNBC groups of patients. Raw and processed data were uploaded to the Gene Expression Omnibus (GEO) database, accession number: GSE141326.

Ozawa P.M., Vieira E., Lemos D.S., Souza I.L., Zanata S.M., Pankievicz V.C., Tuleski T.R., Souza E.M., Wowk P.F., Urban C.D., Kuroda F., Lima R.S., Almeida R.C., Gradia D.F., Cavalli I.J., Cavalli L.R., Malheiros D, & Ribeiro E.M. (2020). Identification of miRNAs Enriched in Extracellular Vesicles Derived from Serum Samples of Breast Cancer Patients. Biomolecules, 10(1), 150.

+ Open protocol

+ Expand

Soft-clip Analysis of Genomic Alterations

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

The genomic DNA from Colo320DM cells was sequenced on Illumina HiSeq 2000 at the University of Chicago Genomics Facility. Sequencing reads were mapped to the human reference genome (hg38) using BWA to create a SAM file. Soft-clipped reads were identified based on the information from CIGAR string. For reads with longer than seven bp soft-clip on any of the ends were considered as real soft-clip reads. By using a 10kb bin to scan across the region from 126425748 to 127997618 in chromosome 8, all the reads in each bin were analyzed and counted to get the ratio of soft-clip reads against the total reads. To assess the statistical significance, the Tukey-Kramer multiple comparison tests were used at the 99 % confidence level.
The whole genomes of mouse C3 and T3 cell lines were sequenced at the Cedars-Sinai Genomics Core. Genomic DNA samples were used to prepare whole genome sequencing libraries using the Ion Xpress Plus Fragment Library Kit (Life Technologies) per manufacturer’s instructions. Final sequencing libraries were sequenced on the Ion Proton System (Life Technologies) using the Ion PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 per manufacturer’s instructions. Raw sequencing reads were aligned to the UCSC mouse reference genome (mm10) and visualized with the integrative genomics viewer (IGV, Broad Institute).

Watanabe T., Marotta M., Suzuki R., Diede S.J., Tapscott S.J., Niida A., Chen X., Mouakkad L., Kondratova A., Giuliano A.E., Orsulic S, & Tanaka H. (2017). Impediment of replication forks by long non-coding RNA provokes chromosomal rearrangements by error-prone restart. Cell reports, 21(8), 2223-2235.

+ Open protocol

+ Expand

RNA-sequencing of Arabidopsis in vitro

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

Three independent biological replicates were produced. For each biological repetition and each point, RNA samples were obtained by pooling RNAs from more than 200 plants. Whole plantlets were collected on plants at 1.04 developmental growth stages (30 (link)), cultivated in vitro under long-day conditions. Total RNA was extracted as described above. RNA-seq experiment was carried out at the POPS Transcriptomic Platform, Institute of Plant Sciences - Paris-Saclay (Orsay, France). PolyA RNA was purified using the Dynabeads mRNA direct micro kit (Ambion, France). The sequencing libraries were constructed with the Ion Total RNA-Seq Kit v2 and the sequencing spheres were prepared with the Ion PI™ Template OT2 200 Kit v3 before sequencing on an Ion Proton using the Ion PI™ Sequencing 200 Kit v3 and Ion PI v2 chips (Life Technologies, France) with 520 run flows.

Pedroza-Garcia J.A., Domenichini S., Mazubert C., Bourge M., White C., Hudik E., Bounon R., Tariq Z., Delannoy E., del Olmo I., Piñeiro M., Jarillo J.A., Bergounioux C., Benhamed M, & Raynaud C. (2016). Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis. Nucleic Acids Research, 44(15), 7251-7266.

+ Open protocol

+ Expand

Globin mRNA Depletion and Whole Transcriptome Sequencing

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

Total RNA was depleted of globin messenger RNA using the GLOBINclear-Human Kit (Life Technologies). Whole transcriptome libraries were made as outlined in the Ion Total RNA-Seq Kit v2 (Life Technologies). Selected libraries were diluted according to the final concentration of 10 pM and clonally amplified using the Ion PI Template OT2 200 Kit v3 (Life Technologies). These amplified libraries were then purified and sequenced on the Ion Proton sequencer for a total of six sequencing runs (Ion PI Chip kit v2) (Life Technologies) according to the manufacturer's instructions.

Hu Y., Zhang K., Zhang T., Wang J., Chen F., Qin W., Tong W., Guan Q., He Y., Gu C., Chen X., Kang U.J., Sun Y.E., Li S, & Jin L. (2020). Exercise Reverses Dysregulation of T-Cell-Related Function in Blood Leukocytes of Patients With Parkinson's Disease. Frontiers in Neurology, 10, 1389.

+ Open protocol

+ Expand

Targeted Sequencing on Ion Proton

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

Sample emulsion PCR, emulsion breaking, and enrichment were performed using the Ion PI Template OT2 200 Kit v3 (Life Technologies, Part #4488318 Rev. B.0), according to the manufacturer’s instructions. Multiple barcoded libraries were combined together with equal molar ratios for one Ion PI v2 chip. 2 pooled Ion AmpliSeq Exome libraries were loaded onto a single Ion PI v2 chip. 5 pooled Ion AmpliSeq Transcriptome libraries were loaded onto a single Ion PI v2 chip. Subsequent emulsion PCR and enrichment of the sequencing beads of the pooled libraries was performed using the Ion OneTouch system (Life Technologies) according to the manufacturer’s protocol within about 7 hours. Finally, 520 Flows sequencing was done on the Ion PI v2 chip using Ion PI Sequencing 200 Kit v3 (Life Technologies, Part #4488315 Rev. B.0) on the Ion Proton sequencer (Life Technologies).

Shin H.Y., Yang W., Lee E.J., Han G.H., Cho H., Chay D.B, & Kim J.H. (2018). Establishment of five immortalized human ovarian surface epithelial cell lines via SV40 T antigen or HPV E6/E7 expression. PLoS ONE, 13(10), e0205297.

+ Open protocol

+ Expand

Ion Torrent Sequencing and HLA Typing

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

Sequencing templates were prepared from the same amounts of the DNA libraries from four to six samples with different individual indices using the Ion PI Template OT2 200 Kit v3 or Ion PI Hi‐Q OT2 200 Kit and an Ion OneTouch system (Life Technologies) according to the manufacturer's instructions. The prepared templates were sequenced using an Ion PI Sequencing 200 Kit v3 or Ion PI HI‐Q Sequencing 200 Kit and the Ion Proton sequencer (Life Technologies). Torrent Suite 4.0 to 5.0 software (Life Technologies) was used to convert the raw signals into base calls and to extract the FASTQ files of the sequencing reads.
Human leucocyte antigen (HLA) typing was performed with the Ion Torrent PGM using a protocol developed in our laboratory (manuscript in preparation).

Nakanishi K., Kukita Y., Segawa H., Inoue N., Ohue M, & Kato K. (2016). Characterization of the T‐cell receptor beta chain repertoire in tumor‐infiltrating lymphocytes. Cancer Medicine, 5(9), 2513-2521.

+ Open protocol

+ Expand

Transcriptome and Proteome Analysis of Muscle Stem Cells

Cited 2 times

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

RNaseq and mass spectrometry measurements were performed as previously described (Zhang et al., 2015 (link)). Briefly, FACS purified MuSC from Chd4^loxP/loxP mice were expanded in vitro and subjected to adenoviral-mediated CRE recombination. Adenovirus encoding GFP served as a control. Samples were generated in biological triplicate and used for RNaseq and mass spectrometric measurements. Total RNA was isolated using commercial kits and according to the manufacturer’s protocol (RNAeasy Mini kit, QIAGEN). RNaseq libraries were constructed using Ion Total RNA-Seq Kit v2 (Life Technologies) and sequencing reactions were performed by Ion Torrent Proton platform with V3 chemistry (Ion PI Template OT2 200 Kit v3, Life Technologies) and PIV2 Chips (Ion PI Chip Kit v2, Life Technologies). For mass spectrometry measurements, whole cell lysates from MuSC obtained from Chd4^loxP/loxP mice were subjected to adenoviral treatment (AdenoCRE/AdenoGFP), the samples were run on SDS-PAGE gels and stained with colloidal protein staining solution (Invitrogen). The gels were evenly sliced and subjected to in-gel digestion with trypsin. Released peptides were measured using a TQ-Orbitrap XL or a LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) equipped with a nanoelectrospray source (Proxeon). Raw data was analyzed using the MaxQuant software package (Cox et al., 2014 (link)).

Sreenivasan K., Ianni A., Künne C., Strilic B., Günther S., Perdiguero E., Krüger M., Spuler S., Offermanns S., Gómez-del Arco P., Redondo J.M., Munoz-Canoves P., Kim J, & Braun T. (2020). Attenuated Epigenetic Suppression of Muscle Stem Cell Necroptosis Is Required for Efficient Regeneration of Dystrophic Muscles. Cell Reports, 31(7), 107652.

+ Open protocol

+ Expand

Small-RNA Sequencing of Pearl Oyster Tissues

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

Eight total RNA samples were extracted from the pearl oyster somatic and gonadal tissues. The subsequent small RNA extraction conformed to the protocol for the mirVana miRNA Isolation Kit (Life Technologies, America). Briefly, the sequencing libraries were constructed as per the Ion Total RNA-seq Kit v2 small-RNA library construction protocol (Life Technologies, America). Adapter ligation, synthesis of cDNA by reverse transcription, purification of the small-RNA fraction, and amplification by PCR were then performed to construct the cDNA libraries. Agilent 2200 Bioanalyzer (Agilent Technologies, Germany) was used for cDNA concentration checking. Using these cDNA libraries, a template for loading onto the analysis chip was prepared according to the protocol of the Ion PI Template OT 2200 Kit v3 (Life Technologies, America). Sequencing was then performed according to the protocol for the Ion Proton system (Ion Proton Sequencer and Ion Proton Torrent Server, Life Technologies, America).

Huang S., Ichikawa Y., Igarashi Y., Yoshitake K., Kinoshita S., Omori F., Maeyama K., Nagai K., Watabe S, & Asakawa S. (2019). Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues. Scientific Reports, 9, 247.

+ 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!