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  • Characterizing the viral genome and host response
  • Identifying and cloning protein targets
  • Expressing and purifying protein targets
  • Immunizing mice and optimizing vaccines

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mRNA and protein therapeutics

  • Characterizing the viral genome and host response
  • Identifying and cloning protein targets
  • Expressing and purifying protein targets
  • Immunizing mice and optimizing vaccines
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Characterizing the viral genome and host response

Respiratory infections are prevalent around the world and impose an enormous health and economic burden. It is essential to understand the nature of the pathogen and diagnose accordingly as soon as possible to prevent its rapid spread and minimize mortality rates. With the advent of molecular biology techniques like genomics, information on these pathogens' identity can be obtained at scale by whole-genome sequencing. This approach includes purifying the pathogen from infected patient samples such as bronchoalveolar fluids, nasal or throat swab, or saliva, and sequencing the pathogen's genome. However, this method poses technical challenges, as pathogen genome content can be scarce and/or degraded. In the case of RNA viruses, researchers need RNA-seq methods that are sensitive and can deal with potentially degraded viral genomic material.

Since the COVID-19 outbreak, researchers worldwide have generated genomics data to define the viral genome and track mutations precisely. The widespread analysis of SARS-CoV-2 genomes, as the epidemic was expanding into a pandemic, allowed researchers to characterize the evolution of the virus. This information is used to deepen our understanding of infection routes and viral sequence variability that might be contributing to the clinical course of the disease. Whole-genome sequencing of SARS-CoV-2 is critical for vaccine design as it provides valuable information on potential antigenic epitopes or new viral variants that could trigger or impair an immune response. This approach is used in reverse vaccinology, which aims to identify promising vaccine candidates through bioinformatics analysis of the viral genome (Bidmos et al. 2018). Our RNA-seq kit SMARTer Stranded total RNA-seq kit v2 (Pico v2; Figure 1) was used for SARS-CoV-2 sequencing in the early stages of the outbreak to provide full-length sequences of the virus (Wu et al. 2019). Examples of published work utilizing SMARTer Stranded RNA-seq technology within workflows for studying and developing vaccines against various pathogens, including coronaviruses, are summarized in a table at the end of this page. We recently launched Pico v3, an improved version of the Pico v2 kit.

Stranded kit features

Figure 1. Transcript expression levels for a 10-ng input amount is shown for the Pico v2 kit. Panel A. Higher reproducibility was observed between 1-ng and 10-ng inputs for data generated with the Pico v2 kit. FPKM values are shown on a log10 scale. Transcripts represented in only one library can be seen along the X- and Y-axes of the scatter plots. Panel B. A summary of the features and benefits of the Pico v2 kit.

In addition to focusing on the viral genome itself, researchers also study the variable regions of T-cell- and B-cell-receptor repertoires of infected patients, providing useful information for identifying novel protective antigens and assess vaccine candidate's efficacy. Studying the immune system of infected patients poses challenges similar to viral genome analysis, as infectious conditions often lead to lymphopenia in patients suffering from viral infections.

Our SMARTer immune profiling kits are used by a number of research groups to assess TCR and BCR repertoire diversity in various disease conditions (see citations below). The features and benefits of the SMARTer TCR and BCR immune profiling kits are summarized below.

Human TCR kit features

Figure 2. Determining sequencing saturation point with the SMARTer human BCR kit's UMI-based error correction gives you more confidence in your clonotype calls and reduces sequencing cost. Panel A. BCR profiling libraries from 10 ng of single-donor PBMC RNA were prepared for this experiment using the SMARTer Human BCR IgG IgM H/K/L Kit. Sequencing saturation for SMARTer human BCR library and IgG clonotype counts at different sequencing depths with (blue line) and without (purple line) UMI-based error correction is shown. With UMIs, you can determine the sequencing saturation point so you don't have to sequence more than needed. All analyses at different sequencing depths were generated with our Takara Bio Immune Profiler Software. Panel B. A summary of the features and benefits of our immune profiling kits.


Citations for products used for viral and host genome sequencing and immune profiling

Title Link Product
SMARTer Stranded total RNA-seq kit (Pico v2)
SARS-CoV-2
SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients SMARTer Stranded total RNA-seq kit v2
Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China
Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany
Genomics functional analysis and drug screening of SARS-CoV-2
Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in Israel
Shared SARS-CoV-2 diversity suggests localised transmission of minority variants
Other viruses
A novel Polycipiviridae virus identified in Pteropus lylei stools SMARTer Stranded total RNA-seq kit v2
High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection
Novel human reovirus isolated from children and its long-term circulation with reassortments
Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus
SMARTer human TCR/BCR profiling kits
Co-activation of macrophages and T cells contribute to chronic GVHD in human IL-6 transgenic humanised mouse model SMARTer Human TCR a/b Profiling Kit
Identification of a neoantigen epitope in a melanoma patient with good response to anti-PD-1 antibody therapy
Clinically relevant cytotoxic immune cell signatures and clonal expansion of T-cell receptors in high-risk MYCN-not-amplified human neuroblastoma
Development of a RACE-based RNA-Seq approach to characterize the T-cell receptor repertoire of porcine γδ T cells
Recovery and assessment of leukocytes from LR Express filters
Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens
Genomic profiling of intestinal T-cell receptor repertoires in inflammatory bowel disease

Featured products

Cat. # Product Size Price License Quantity Details
634485 SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian 24 Rxns USD $2685.00

License Statement

ID Number  
425 LIMITED USE LABEL LICENSE: RESEARCH USE ONLY Notice to Purchaser: This product is the subject to a license granted to Takara Bio USA, Inc. and its Affiliates from Caribou Biosciences, Inc., and this product is transferred to the end-user purchaser (“Purchaser”) subject to a “Limited Use Label License” conveying to the Purchaser a limited, nontransferable right to use the product, solely as provided to Purchaser, together with (i) progeny or derivatives of the product generated by the Purchaser (including but not limited to cells), and (ii) biological material extracted or derived from the product or its corresponding progeny or derivatives (including but not limited to cells) (collectively, the product, and (i) and (ii) are referred to as “Material”) only to perform internal research for the sole benefit of the Purchaser. The Purchaser cannot sell or otherwise transfer Material to a third party or otherwise use the Material for any Excluded Use. “Excluded Use” means any and all: (a) commercial activity including, but not limited to, any use in manufacturing (including but not limited to cell line development for purposes of bioproduction), product testing, or quality control; (b) preclinical or clinical testing or other activity directed toward the submission of data to the U.S. Food and Drug Administration, or any other regulatory agency in any country or jurisdiction where the active agent in such studies comprises the Material; (c) use to provide a service, information, or data to a third party with the sole exception of using the Material to conduct in vitro sample preparation, i.e., selectively depleting target cDNAs from a sample either by cleaving or selectively separating such target cDNAs from the sample through the use of the Materials; (d) use for human or animal therapeutic, diagnostic, or prophylactic purposes or as a product for therapeutics, diagnostics, or prophylaxis; (e) activity in an agricultural field trial or any activity directed toward the submission of data to the U.S. Department of Agriculture or any other agriculture regulatory agency; (f) high throughput screening drug discovery purposes (i.e., the screening of more than 10,000 experiments per day) as well as scale-up production activities for commercialization; (g) modification of human germline, including editing of human embryo genomes (with the sole exception of editing human embryonic stem (ES) cell lines for research purposes) or reproductive cells; (h) self-editing; and/or (i) stimulation of biased inheritance of a particular gene or trait or set of genes or traits (“gene drive”). It is the Purchaser’s responsibility to use the Material in accordance with all applicable laws and regulations. For information on obtaining additional rights, including commercial rights, please contact licensing@cariboubio.com or Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA 94710 USA, Attn: Licensing
392 This Product is protected by one or more patents from the family consisting of:US10941397, People's Republic of China Patent: ZL201480057094.4, US10781443, US10954510, DE602014069266.4, EP3058104, FR3058104, UK3058104, JP6602294, SE3058104, CA2923812, and any corresponding patents, divisionals, continuations, patent applications and foreign filings sharing common priority with the same family. Information on relevant patents and licenses for this product may be found at: https://www.takarabio.com/patents. 
395
This Product is protected by one or more patents from the family consisting of: US10150985, CA2939621, People's Republic of China Patent: ZL201480077658.0, US10988796, DE602014058059.9, EP3105325, FR3105325, UK3105325, JP6416939 and any corresponding patents, divisionals, continuations, patent applications and foreign filings sharing common priority with the same family.  Additional information may be found at https://www.takarabio.com/patents. 
450 This Product is sold under license from JumpCode Genomics, Inc., and is covered by one or more of the following US patents and foreign counterparts as well as pending US and foreign patent applications: 10,604,802; 11,708,606; 11,761,039; PCT/US2015/014242; CA2938669; EP 20192599.7; HK402021031164.3.
455 This product is sold under license from Becton Dickinson and Co., and may be the subject of U.S. Patent Nos.: 8,835,358; 9,290,809; 9,315,857; 9,708,659; 9,845,502; 10,047,394; 10,059,991; 10,202,646; 10,392,661; 10,619,203; 11,970,737; 12,060,607; and its foreign counterparts.

The SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian is used to generate strand-specific RNA-seq libraries for Illumina sequencing from 250 pg–10 ng inputs of purified total RNA or from 10–1,000 intact cells. This kit incorporates Takara Bio’s proprietary SMART (Switching Mechanism at the 5’ end of RNA Template) technology and includes refinements to the SMARTer method for stranded RNA-seq that simplify the library preparation workflow and improve sequencing performance. This method was developed to work with either high- or low-quality total RNA, does not require additional rRNA removal methods or kits, and produces sequencing libraries that retain strand-of-origin information. The integrated removal of cDNAs derived from rRNA—typically present in high abundance following cDNA synthesis from total RNA inputs—makes the workflow extremely sensitive, yielding data that is highly reproducible with low mapping to rRNA. The new library design featured in this updated kit adds an 8 nucleotide (nt) unique molecular identifier (UMI) through the reverse-transcription step to mitigate potential PCR bias as well as to provide customers with additional information for transcript quantification, specifically for true variants and rare mutations. This kit includes the SMARTer RNA Unique Dual Index Kit - 24U (Takara Bio, Cat. No. 634451). SMARTer RNA Unique Dual Index Kit – 96U Set A and B (Cat. #s 634452, and 634457) are available for purchase. Together they offer up to 192 unique dual indexes for multiplexing.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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634485: SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian

634485: SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian
634467 SMARTer® Human BCR IgG IgM H/K/L Profiling Kit 48 Rxns USD $3496.00

License Statement

ID Number  
325 Patent pending. For further information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
455 This product is sold under license from Becton Dickinson and Co., and may be the subject of U.S. Patent Nos.: 8,835,358; 9,290,809; 9,315,857; 9,708,659; 9,845,502; 10,047,394; 10,059,991; 10,202,646; 10,392,661; 10,619,203; 11,970,737; 12,060,607; and its foreign counterparts.

The SMARTer Human BCR IgG IgM H/K/L Profiling Kit enables users to analyze B-cell receptor (BCR) repertoires from total RNA samples. This kit can generate libraries from 10 ng to 1 µg of total RNA from peripheral blood mononuclear cells (PBMCs) and 1 to 100 ng of total RNA from B cells. This kit may be used for other sample types, but the protocol may need to be modified. The kit can be used to generate data for both heavy and light chains (kappa and lambda) of human immunoglobulin IgG and IgM.

The SMARTer Human BCR IgG IgM H/K/L Profiling Kit leverages SMART technology and employs a 5' RACE-like approach to capture complete V(D)J variable regions of BCR transcripts. It also incorporates unique molecular identifiers (UMI) to facilitate PCR error correction and clonotype quantification during data analysis.

Included in the kit are primers that incorporate Illumina-specific adapter sequences during cDNA amplification. The protocol generates indexed libraries that are ready for sequencing on Illumina platforms. This kit supports up to 48 rxns.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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634467: SMARTer Human BCR IgG IgM H/K/L Profiling Kit

634467: SMARTer Human BCR IgG IgM H/K/L Profiling Kit
634478 SMARTer® Human TCR a/b Profiling Kit v2 12 Rxns USD $1578.00

License Statement

ID Number  
455 This product is sold under license from Becton Dickinson and Co., and may be the subject of U.S. Patent Nos.: 8,835,358; 9,290,809; 9,315,857; 9,708,659; 9,845,502; 10,047,394; 10,059,991; 10,202,646; 10,392,661; 10,619,203; 11,970,737; 12,060,607; and its foreign counterparts.

The SMARTer Human TCR a/b Profiling Kit v2 enables users to analyze T-cell receptor (TCR) repertoires from bulk RNA samples. This kit can generate libraries from total RNA (10 ng to 1 µg from peripheral blood leukocytes, 20 ng to 200 ng of total RNA obtained from whole blood, or 1 ng to 100 ng T cells) or purified T cells (1,000 to 10,000 cells) and can be used to generate data for both TCR-alpha or TCR-beta subunits. Unique molecular identifiers (UMIs) are incorporated to facilitate PCR error correction and clonotype quantification during data analysis, and unique dual indexes (UDIs) allow users to multiplex more samples and to provide confidence when sequencing on patterned flow cells. At the end, generated indexed libraries are ready for sequencing on Illumina platforms.

This kit supports up to 12 rxns.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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Sensitive and reproducible clonotype detection from a broad range of sample types and RNA amounts.

Sensitive and reproducible clonotype detection from a broad range of sample types and RNA amounts.

Variable and highly complex samples are accommodated without the need for RNA purification or T-cell enrichment. TRA and TRB libraries were generated from 1, 10, and 100 ng of human CD3+ T‑cell total RNA (Panel A), 1,000 and 10,000 CD3+ T cells (Panel B), and 20 ng of whole-blood RNA extracted from three different samples (Panel C). The sequence reads were processed by Cogent NGS Immune Profiler.

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The Takara Bio TCR profiling kit identifies a wide range of clonotype counts.

The Takara Bio TCR profiling kit identifies a wide range of clonotype counts.

The number of clonotypes detected reveals biological variation. Duplicate libraries were generated from 10 ng RNA extracted from single-donor PBMC samples (P1-P6) and sequenced on an Illumina MiSeq system using 300-bp paired-end reads to obtain approximately 1.5 million reads per sample. Resulting sequencing reads were processed with Cogent NGS Immune Profiler. Clonotype numbers from different donors for TRA (blue) and TRB (orange) are shown. Error bars shown represent the standard error between the duplicates.

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The Takara Bio TCR profiling kit generates data with sensitivity superior to competitors

The Takara Bio TCR profiling kit generates data with sensitivity superior to competitors
A dramatically higher clonotype number was observed for TRB after downsampling. (TRA results were similar; data not shown.) 5M PBMC cells were split from two different healthy donors for RNA and gDNA extraction. 1.6 g of gDNA (15% of the total amount of extracted gDNA) was used for library preparation according to manufacturer's instructions. 100 ng of RNA (2% of the total amount of extracted RNA) was used for library preparation.

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634478: SMARTer Human TCR a/b Profiling Kit v2

634478: SMARTer Human TCR a/b Profiling Kit v2

Takara Bio USA, Inc.
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Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, Takara Bio USA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES (EXCEPT AS SPECIFICALLY NOTED).

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Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, Takara Bio USA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

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