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  • Characterizing the viral genome and host response
  • Identifying and cloning protein targets
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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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Immunizing mice with vaccine targets and further optimization

An animal model's ability to reproduce relevant human physiology determines its utility and appropriateness for vaccine development. Good animal models share the same physiological characteristics as humans or reflect them as closely as possible. Using preclinical animal models that express the required receptors for a specific pathogen—or natural disease models with pathology comparable to the human disease—remains critical prior to vaccine testing in humans.

Typically, natural or surrogate animal models are used for vaccine development. Natural disease models have the advantage of modeling the interaction between host and pathogen within the appropriate biological context and make use of a specific pathogen and its natural host. Surrogate models refer to the use of species that can only be infected with the pathogen of interest under experimental conditions. Compromises such as higher infection doses or artificial routes of infection often have to be made with surrogate models, but they have provided a useful tool for studying specific aspects of either disease pathogenesis or the host's immune response. In most cases, mice are the animal species of choice. Mouse models offer the advantage of working in a consistent genetic background, are easy to handle, and are relatively cost effective (Gerdts et al. 2007).

Takara Bio's SMARTer Mouse BCR and TCR profiling kits help speed up the process of immune sera screening of mice for antiviral activity of target vaccines by monitoring vaccine-specific changes in the BCR and TCR clonotype repertoires as a proxy for an efficient immune response to the vaccine challenge. Promising vaccine candidates are further optimized by analyzing and comparing antibody and T-cell responses in the vaccinated animals prior to and upon exposure to the virus.

Watch a webinar about mouse T-cell receptor repertoire profiling using the SMARTer kit

Benefits

  • Complete V(D)J sequence information—obtain full-length sequences for variable regions of TCR mRNA transcripts
  • TCR-alpha and TCR-beta—profile diversity for both TCR subunits, either in the same experiment or separately
  • No multiplex PCR required—amplify sequences for each TCR subunit with a single primer pair per reaction
  • Illumina-ready sequencing libraries—incorporate Illumina adapter and index sequences in a ligation-independent manner, and multiplex up to 96 libraries in a single flow-cell lane

 


Numerous laboratories have already used SMARTer BCR and TCR profiling kits for their vaccine development research:

Title Link Product
TCR profiling
Extremely strong infiltration of WT1-specific CTLs into mouse tumor by the combination vaccine with WT1-specific CTL and helper peptides SMARTer Mouse TCR a/b Profiling Kit
A liposomal RNA vaccine inducing neoantigen-specific CD4+ T cells augments the antitumor activity of local radiotherapy in mice
Irreversible electroporation combined with checkpoint blockade and TLR7 stimulation induces antitumor immunity in a murine pancreatic cancer model.
BCR profiling
Programmed Death-1 Restrains the Germinal Center in Type 1 Diabetes SMARTer Mouse BCR IgG H/K/L Profiling Kit

References

Gerdts, V., Littel-van den Hurk, S. D., Griebel, P. J., Babiuk, L. A. Use of Animal Models in the Development of Human Vaccines. Future Microbiol. 2, 667–675 (2007). 


Featured products

Cat. # Product Size Price License Quantity Details
634402 SMARTer® Mouse TCR a/b Profiling Kit 12 Rxns USD $986.00

License Statement

ID Number  
275 SMART-Seq2 Technology. This product is sold under exclusive license from Ludwig Institute of Cancer Research, Ltd. and is covered by US Patent No. 10266894, Japanese Patent No. 6336080, and European Patent No. 3036336, and pending U.S. patent application and/or pending claims of foreign counterparts. For license information, please contact a Takara Bio USA, Inc. licensing representative by e-mail at licensing@takarabio.com.

The SMARTer Mouse TCR a/b Profiling Kit provides a powerful new solution for those seeking to perform T-cell receptor (TCR) repertoire analysis using NGS.

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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Library preparation workflow and PCR strategy for TCR profiling using the SMARTer approach

Library preparation workflow and PCR strategy for TCR profiling using the SMARTer approach
Library preparation workflow and PCR strategy for TCR profiling using the SMARTer approach. Panel A. Reverse transcription and PCR amplification of TCR subunit mRNA sequences. First-strand cDNA synthesis is primed by the TCR dT Primer and performed by an MMLV-derived reverse transcriptase (RT). Upon reaching the 5′ end of each mRNA molecule, the RT adds non-templated nucleotides to the first-strand cDNA. The SMART-Seq v4 Oligonucleotide contains a sequence that is complementary to the non-templated nucleotides added by the RT, and the oligo hybridizes to the first-strand cDNA. In the template-switching step, the RT uses the remainder of the SMART-Seq v4 Oligonucleotide as a template for the incorporation of an additional sequence on the end of the first-strand cDNA. Full-length variable regions of TCR cDNA are selectively amplified by PCR using primers that are complementary to the oligonucleotide-templated sequence (SMART Primer 1) and the constant region(s) of TCR-α and/or TCR-β subunits (TCRa and/or TCRb Mouse Primer 1). A subsequent round of PCR is performed to further amplify variable regions of TCR-α and/or TCR-β subunits and incorporate adapter sequences using a TCR Primer 2 Forward HT Index and a TCRa and/or TCRb Mouse Primer 2 Reverse HT Index. Included in the primers are adapter and index sequences (Read 2 + i7 + P7 and Read 1 + i5 + P5, respectively) that are compatible with the Illumina sequencing platform. Following purification, size selection, and quality analysis, the TCR cDNA library is ready for sequencing. Panel B. Semi-nested PCR approach for amplification of TCR-α and/or TCR-β subunits. The primer pairs used for the first round of amplification capture the entire variable region(s) and most of the constant region(s) of TCR-α and/or TCR-β cDNA. The second round of amplification retains the entire variable region(s) of TCR-α and/or TCR-β cDNA and a smaller portion of the constant region(s). The anticipated size of the final TCR library cDNA (inserts + adapters) is ~700–800 bp.

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Assessment of TCR diversity in mouse spleen samples with the SMARTer Mouse TCR a/b Profiling Kit

Assessment of TCR diversity in mouse spleen samples with the SMARTer Mouse TCR a/b Profiling Kit
Assessment of TCR diversity in mouse spleen samples with the SMARTer Mouse TCR a/b Profiling Kit. Panel A. To compare TCR diversity between the spleen's general T-cell population and purified CD4+ T cells, total splenocytes were isolated from spleen and divided into two groups. The first group was left untouched, and the second group was subject to CD4+ T-cell purification (see Methods section for details). Total RNA was extracted from the total splenocyte group and the group enriched for CD4+ T cells, and each RNA sample was used for library preparation. Panel B. Proportion of on-target reads mapping to TCR-α or TCR-β CDR3 sequences. Panel C. Rarefaction curves showing the relationship between read depth and the number of unique clonotypes identified for TCR-α (left) and TCR-β (right). When a curve starts to flatten off, the number of unique clonotypes identified is reaching saturation. Dashed lines show the theoretical number of clonotypes as the number of reads increases.

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Assessment of TCR-α clonotype diversity in various tissues of transgenic mice of different ages with the SMARTer Mouse TCR a/b Profiling Kit

Assessment of TCR-α clonotype diversity in various tissues of transgenic mice of different ages with the SMARTer Mouse TCR a/b Profiling Kit
Assessment of TCR-α clonotype diversity in various tissues of transgenic mice of different ages with the SMARTer Mouse TCR a/b Profiling Kit. Panel A. The percentage of reads mapping to TCR-α CDR3 sequences identified in the thymus, spleen, peripheral lymph nodes (PLN), mesenteric lymph nodes (MLN), and large intestine (LI) is consistent across the 16-week-old, 34-week-old, and 38-week-old mice. Panel B. The immune tissues showed the highest TCR-α clonotypic diversity, while the large intestine showed the lowest diversity. This indicates that the large intestine has the lowest T-cell infiltrate. Panel C. Abundance of the TRAV3-2-TRAJ58 clonotype, expressed as a percentage of all reads mapping to any TCR-α or TCR-β clonotype, across tissue types and ages. Panel D. Abundance of the TRAV16N-TRAJ56 clonotype, expressed as a percentage of all reads mapping to any TCR-α or TCR-β clonotype, across tissue types in the 38-week-old mouse.

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634402: SMARTer Mouse TCR a/b Profiling Kit

634402: SMARTer Mouse TCR a/b Profiling Kit
634422 SMARTer® Mouse BCR IgG H/K/L Profiling Kit 12 Rxns USD $986.00

The SMARTer Mouse BCR IgG H/K/L Profiling Kit enables users to analyze B-cell receptor (BCR) diversity from total RNA samples and whole cells. This kit is designed to work with a range of RNA inputs, from 10 ng to 3 µg of total RNA obtained from 1,000 to 10,000 purified B cells. This kit can be used to generate data for both heavy (IgG only) and light chain diversity. The kit is not intended to identify the subclasses of IgG heavy chain that are expressed (i.e., IgG1, IgG2a, IgG2b, IgG2c, or IgG3).

This kit leverages SMART technology and employs a 5' RACE-like approach to capture complete V(D)J variable regions of BCR transcripts. Included in the kit are primers that incorporate Illumina-specific adaptor sequences during cDNA amplification. 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.

Documents Components Image Data

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634422: SMARTer Mouse BCR IgG H/K/L Profiling Kit

634422: SMARTer Mouse BCR IgG H/K/L Profiling Kit

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BCR development.

BCR development.

BCR development. The progenitor cell undergoes recombination of V, D, and J segments in the germline, which generates two identical heavy chains. Recombination of V and J segments generates two identical light chains. Random nucleotide additions or deletions at the junctions of the V, D, and J segments provide additional diversity. Furthermore, B cells activated by immune responses undergo somatic hypermutation (SHM), in which additional point mutations are introduced.

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SMARTer Mouse BCR IgG H/K/L Profiling Kit workflow.

SMARTer Mouse BCR IgG H/K/L Profiling Kit workflow.

SMARTer Mouse BCR IgG H/K/L Profiling Kit workflow. Panel A. First-strand cDNA synthesis is dT-primed (BCR dT Primer) and performed by the MMLV-derived SMARTScribe Reverse Transcriptase (RT), which adds nontemplated nucleotides upon reaching the 5' end of each mRNA template. The BCR Oligonucleotide anneals to these nontemplated nucleotides and serves as a template for the incorporation of an additional sequence of nucleotides into the first-strand cDNA by the RT (this is the template-switching step). The BCR Oligonucleotide contains sequence from the Illumina Read Primer 2, serving as a primer-annealing site for subsequent rounds of PCR, and ensuring that only sequences from full-length cDNAs undergo amplification. Panel B. The first PCR uses the first-strand cDNA as a template and includes a forward primer with complementarity to the Illumina Read Primer 2 sequence (BCR Primer 1V), and a reverse primer that is complementary to the constant (i.e., nonvariable) region of BCR heavy or light chains (mBCR Primers 1H, 1K, or 1L). The chains are amplified in separate reactions. By priming from the Read Primer 2 sequence and the constant region, the first PCR specifically amplifies the entire variable region and a considerable portion of the constant region of BCR heavy or light chain cDNA. The second PCR takes the product from the first PCR as a template and uses semi-nested primers (mBCR Primers 2H, 2K, or 2L) to amplify the entire variable region and a portion of the constant region of BCR heavy or light chain cDNA. As in PCR 1, the BCR subunit chains are amplified in separate reactions.

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Highly specific amplification of Ig chains.

Highly specific amplification of Ig chains.

Highly specific amplification of Ig chains. Libraries containing BCR G and K chain transcripts were generated using the SMARTer Mouse BCR IgG H/K/L Profiling kit, starting with 10 ng of RNA isolated from a hybridoma developed in-house (10E8) and two manufactured ATCC hybridoma samples (HB-8117 and TIB-127). Panel A. Bioanalyzer traces showing gene-specific amplification of G, K and L chains for each hybridoma. Peaks labeled "LM" and "UM" correspond to DNA reference markers included in each analysis. Panel B. Mapping metrics were determined using MiXCR software (version 2.1.81.8; software not provided with kit) and aligned against all Ig reference sequences, with a clone fraction threshold of 0.01%. V, D, and J IMGT allele outputs, alignment scores and consensus CDR3 amino acid CDR3 for the top heavy (G) and light (K) chain clone for each hybridoma are displayed. For cases in which the MiXCR software determined the presence of more than one V, D, or J allele, all determined alleles with alignment scores are shown.

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PCR cycling and pooling workflow.

PCR cycling and pooling workflow.

PCR cycling and pooling workflow. After RT step, the user amplifies the G, K, or L chain transcripts in separate reactions. Each amplification uses 5 µl of the RT reaction. Following the first PCR, 1 µl of each PCR is used in a separate PCR reaction (PCR 2) to add the same sequencing indexes to each amplified chain for a given sample, but distinct indexes for each different sample. After this final amplification in PCR2, the user may validate each product on a Bioanalyzer or other fragment analysis system. The user then has the flexibility to choose which amplified BCR chains to pool for sequencing.

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Effect of PCR pooling strategy on Ig alignment rate and clonotype identification.

Effect of PCR pooling strategy on Ig alignment rate and clonotype identification.

Effect of PCR pooling strategy on Ig alignment rate and clonotype identification. G and K chain PCR products (GK) or G, K and L chain PCR products (GLK) were pooled and sequenced for each hybridoma sample. Panel A. The percentage of reads aligning to Ig reference sequences for GK pooling, GKL pooling, and L only sequencing strategies as determined by MiXCR software. Panel B. The identified CDR3 amino acid consensus sequence and percent distribution for the top heavy (G) and light (K) chain clone for GK pooling or GKL pooling strategies as determined by the MiXCR software. The clone fraction threshold was set to 0.01%.


SMARTer Mouse TCR a/b Profiling Kit—obtain full-length sequences of TCR-alpha and TCR-beta V(D)J variable regions

The SMARTer Mouse TCR a/b Profiling Kit provides a powerful new solution for those seeking to perform T-cell receptor (TCR) repertoire analysis using NGS.

View data

SMARTer Mouse BCR IgG H/K/L Profiling Kit—capturing complete V(D)J variable regions of BCR transcripts

5’ RACE is paired with NGS technology to provide a sensitive, accurate, and optimized approach to BCR profiling.

View data

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