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  • ‹ Back to Immune Profiling
  • Track B-cell changes in your mouse model
  • Efficient and sensitive profiling of human B-cell receptor repertoire
  • TCRv2 kit validated for rhesus macaque samples
  • Improved TCR repertoire profiling from mouse samples (bulk)
  • TCR repertoire profiling from mouse samples (bulk)
  • BCR repertoire profiling from mouse samples (bulk)
  • Improved TCR repertoire profiling from human samples (bulk)
  • TCR repertoire profiling from human samples (single cells)
  • BCR repertoire profiling from human samples (bulk)
SMARTer NGS for TCR SMARTer Human TCR a/b Profiling Kit v2
SMARTer TCRv2 technical note View data generated with the TCRv2 kit
Home › Learning centers › Next-generation sequencing › Technical notes › Immune Profiling › TCRv2 kit validated for rhesus macaque samples

Technical notes

  • DNA-seq
    • Next-gen WGA method for CNV and SNV detection from single cells
    • Low-input whole-exome sequencing
    • DNA-seq from FFPE samples
    • Low cell number ChIP-seq using ThruPLEX DNA-Seq
    • Detection of low-frequency variants using ThruPLEX Tag-Seq FLEX
    • ThruPLEX FLEX outperforms NEBNext Ultra II
    • Streamlined DNA-seq from challenging samples
    • High-resolution CNV detection using PicoPLEX Gold DNA-Seq
    • ThruPLEX FLEX data sheet
    • Low-volume DNA shearing for ThruPLEX library prep
    • NGS library prep with enzymatic fragmentation
    • Comparing ThruPLEX FLEX EF to Kapa and NEBNext
  • Immune Profiling
    • Track B-cell changes in your mouse model
    • Efficient and sensitive profiling of human B-cell receptor repertoire
    • TCRv2 kit validated for rhesus macaque samples
    • Improved TCR repertoire profiling from mouse samples (bulk)
    • TCR repertoire profiling from mouse samples (bulk)
    • BCR repertoire profiling from mouse samples (bulk)
    • Improved TCR repertoire profiling from human samples (bulk)
    • TCR repertoire profiling from human samples (single cells)
    • BCR repertoire profiling from human samples (bulk)
  • Epigenetic sequencing
    • ChIP-seq libraries for transcription factor analysis
    • ChIP-seq libraries from ssDNA
    • Full-length small RNA libraries
    • Methylated DNA-seq with MBD2
  • Reproductive health technologies
    • Embgenix ESM Screen
    • Embgenix PGT-A
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SMARTer NGS for TCR SMARTer Human TCR a/b Profiling Kit v2
SMARTer TCRv2 technical note View data generated with the TCRv2 kit
Technical note

Highly reproducible TCR profiling using RNA from rhesus macaque PBMC

NOTE: SMART-Seq Human TCR (with UMIs) is an equivalent replacement for the SMARTer Human TCR a/b Profiling Kit v2 with minor updates. (See a complete list of kits with new names and the existing kits they will replace here). The update does not in any way impact the protocols or functional performance of these kits.

Non-human primates (NHP) such as the rhesus macaque (Macaca mulatta) have long been key translational models in biomedical research because of their genetic and physiological similarity to humans. Studies using rhesus macaques have contributed significantly to our understanding of T-cell responses to vaccines, cancer, and infectious diseases including HIV. More recently, these NHP have emerged at the forefront of COVID-19 vaccine research.

Increasingly complex information can now be gleaned from immune system processes. High-throughput TCR sequencing (TCR-seq) profiles T-cell responses in exquisite detail. A comprehensive understanding of immune responses in such a closely related organism as the rhesus macaque would be a significant advance in science.

Numerous tools exist for performing TCR-seq in human samples, but equivalent tools for rhesus samples have been lacking. Because rhesus macaques often serve as surrogates in the lead-up to human studies, there is an industry need for a complete TCR-seq solution for these NHP samples. 

Due to strong species homology, our SMARTer Human TCR a/b Profiling Kit v2 (TCRv2) can generate high quality TCR sequencing libraries using human or rhesus macaque RNA.

Industry-leading features of TCRv2 include:

  • UMI-based correction: removes reads derived from PCR duplicates and sequencing errors
  • Adaptable data output: sequence either full-length V(D)J or CDR3 information
  • UDI implementation: increased multiplexing and confidence on high-throughput sequencers
  • High sensitivity and reproducibility: identify rare clonotypes with certainty
  • Validated species flexibility: use with human and rhesus macaque RNA samples
Introduction Results Conclusion Materials and methods References

Introduction  

Genetic basis of the T-cell repertoire

In humans and NHP, T cells are an essential component of adaptive immunity. On the surface, each T cell expresses a unique T-cell receptor (TCR) to recognize a specific antigen. Each TCR is a heterodimer. About 95% of T-cells have TCRs composed of an alpha and beta chain. The remaining 5% have TCRs composed of delta and gamma chains. 

TCR are encoded by the TRA and TRB genes in the case of αβ T cells, or TRG and TRD genes in the case of ɣ∂ T cells. All of these genes are organized into clusters of segments representing the variable (V), diversity (D; TRB/TRD only), joining (J), and constant (C) regions of the TCR. Developing T cells undergo V(D)J recombination in which single V, D, J, and C gene segments are recombined into mature TRA and TRB loci (or TRG and TRD loci). From these, TCRα and TCRβ chains (or TCRɣ and TCR∂) are expressed. Each clonal population of T cells shares a clonotype, or distinguishing set of loci.

The TCR repertoire—that is, the diverse collection of clonotypes in an organism—plays a major role in shaping immune function, health, and disease progression. Over the last decade, next generation sequencing (NGS) approaches are increasingly used to profile human TRA and TRB genes. Researchers often choose to maximize information by sequencing full-length genes. For high-throughput NGS projects where speed and cost-efficiency are needed, researchers may choose to focus on the CDR3-encoding region of the TRB gene. This region, which contacts the antigen, is the most variable (Figure 1).

Figure 1. T-cell receptor structure and diversification. A functional αβ TCR heterodimer consisting of α- and β-subunit chains, with the "variable" (V), "joining" (J), and "constant" (C) segments depicted in magenta, blue, and green, respectively. The TCR-β subunit chains include these and an additional "diversity" (D) segment, depicted in orange. The CDR3 region of the TCRβ subunit is labeled.

The constant regions of the TRA and TRB genes in human and rhesus macaque share significant homology. Therefore, it is likely that tools used to track human T-cell repertoire dynamics can do the same in the rhesus macaque.

SMARTer Human TCR a/b Profiling Kit v2 chemistry 

Since the recombined V(D)J segments are located in a region extending to the 5' ends of the TRA and TRB genes, capture of full RNA transcript information is essential for immune profiling. The TCRv2 kit employs SMART (Switching Mechanism at 5' end of RNA Template) technology combined with a 5'-RACE approach. This method ensures efficient incorporation of an RNA's 5'-end via the template-switching mechanism.

Briefly, the SMARTScribe Reverse Transcriptase adds a sequence of nontemplated nucleotides the 5' end of the cDNA. The TCR SMART UMI Oligo (TSUO) binds to these nontemplated nucleotides and also adds the unique molecular identifiers (UMIs). This template-switching step ensures efficient capture of the 5' end of RNA template. Full-length cDNA can be obtained by a combination of the TSUO, the highly efficient long-distance reverse transcriptase, and the use of high-integrity RNA as input.

Subsequent rounds of TCR-specific, nested PCR cycles, depicted in Figure 2, Panel A, amplify the V(D)J portions of the TRA and TRB sequences. These steps rely on primers binding to conserved sequences in the constant regions of TRA and TRB. During the PCR 2 step, unique dual indexes (UDIs) are added. Figure 2, Panel B shows a zoomed-in schematic view of these locations. Sequence homology allows TCRv2 chemistry to amplify rhesus macaque transcripts in an accurate and unbiased manner during both PCR steps.

Figure 2. SMARTer Human TCR a/b Profiling Kit v2 workflow—when rhesus macaque RNA input was used, no changes were made to accommodate the change of species. Panel A. First-strand cDNA synthesis is dT-primed and performed by the MMLV-derived SMARTScribe Reverse Transcriptase (RT), which adds proprietary nontemplated nucleotides (XXXXX) upon reaching the 5' end of each mRNA template. The TCR SMART UMI Oligo anneals to these nontemplated nucleotides, allowing it to serve as a template for the incorporation of the SMART Sequence (light green) and UMI (yellow) at the 5' end of each cDNA molecule by the RT. This is the template-switching step. The resulting cDNA then undergoes two rounds of TCR-specific PCR amplification. In the PCR 1 step, the forward primer (hTCR PCR1 Universal Forward) anneals to the SMART Sequence (light green) and adds the Read 2 sequence (dark green). The reverse primer (hTCRa/hTCRb PCR1 Reverse, orange) anneals near the 3' end of the TRA/TRB transcript, within the constant region (see details in Panel B). The PCR 2 step uses the PCR 1 product as a template. PCR 2’s forward primer has complementarity to the SMART Sequence (light green) and Read 2 sequence (dark green) and adds Unique Dual Indexes (UDIs, dark blue). PCR 2 uses semi-nested reverse primers. One reverse primer (hTCRa/hTCRb PCR2 UDI Reverse) anneals to an upstream portion (red) of the constant region relative to PCR 1’s reverse primer (orange) and it adds the Read 1 sequence (lavender). The other reverse primer has complementarity to the Read 1 sequence (lavender) and adds UDIs (dark blue). Thus, a sequencing-ready library of TRA and TRB transcripts is created. Panel B. A more detailed view shows the approximate annealing locations of all PCR 1 and PCR 2 primers within the V(D)J and constant regions of the TRA and TRB sequences. By priming from the SMART Sequence and the constant region, the PCR 1 step ensures the capture of the entire V(D)J region and specifically amplifies all TRA/TRB transcripts in an unbiased manner. The PCR 2 step further enriches TRA/TRB transcripts, adds UDIs, and decreases amplicon size, facilitating read-through on Illumina instruments. The UDIs include adapter and index sequences that are compatible with Illumina sequencing platforms and allow for multiplexing of up to 192 samples in a single flow cell lane. 

Results  

SMARTer Human TCR a/b Profiling Kit delivers robust and reproducible TCR capture from rhesus macaque RNA input

To test the compatibility of the TCRv2 kit with rhesus macaque RNA, samples from rhesus macaque and human donors were processed in parallel, with no changes to the TCRv2 kit protocol. The TRA and TRB gene homology between rhesus macaque and human precluded any need to change the kit's components. To cover the high and low ends of the RNA input range, 10 ng and 100 ng were chosen as the amounts of starting material. In this case, the sources were total RNA isolated from peripheral blood mononuclear cells (PBMC) of three rhesus macaques or from the control supplied with the TCRv2 kit, Human Blood, Peripheral Leukocytes Total RNA (hereafter referred to as hCtrl).

Libraries were generated in triplicate from each of the rhesus macaque donors or from hCtrl, using high-quality RNA (RIN ≥8). Hereafter, libraries made from 10 ng RNA from rhesus macaque PBMC are referred to as RM-10 while those made from 100 ng are called RM-100.

For both human and rhesus macaque libraries, Bioanalyzer traces showed an amplicon size distribution of 650–1,150 bp, with an average peak size of roughly 690 bp, as would be expected for this type of cDNA sample. Figure 3 shows electroherograms of the SMARTer TCR libraries generated from hCtrl (Panel A) and PBMC RNA from a rhesus macaque (Panel B).

Figure 3. TCR sequencing libraries with similar size distributions are produced from human and rhesus macaque RNA inputs. TRA/TRB mixed libraries were prepared using 100 ng total RNA isolated from PBMC of human (Panel A) or a rhesus macaque donor (Panel B). Completed libraries were run through the Agilent 2100 Bioanalyzer system.

Clonotype capture from rhesus PBMC RNA using the TCRv2 kit is highly reproducible across input levels

The number of clonotypes detected was dependent on the quantity of starting RNA provided (Figure 4, Panel A). Clonotype counts from the TRA and TRB libraries consistently increase as the amount of RNA input increases. Regardless of input amount, the finished TRA/TRB libraries made from rhesus macaque PBMC were highly reproducible, with strong correlation between technical replicates. Analysis of overlapping clones revealed Pearson correlation scores of at least 0.9 for TRA and 0.96 for TRB (Figure 4, Panels B and C). This matches the high standard set by TRA/TRB libraries generated from human RNA samples using the TCRv2 kit, which had Pearson correlation scores of at least 0.91 for TRA and 0.97 for TRB.

Figure 4. TCRv2 sequencing libraries from rhesus macaque samples show highly reproducible clonotype detection. RM-10 and RM-100 libraries were created in triplicate from PBMC of three rhesus macaque donors. Full-length TRA and TRB sequences were obtained using the Illumina MiSeq® platform. Average reads/sample were 3 million for RM-10 and 1 million for RM-100. Clonotypes were identified using Cogent NGS Immune Profiler v1 software. The total number of clonotypes per input amount and gene target were identified in one representative donor (Panel A). Error bars represent the standard deviation among triplicates. Two replicates from a representative donor’s RM-10 (Panel B) and RM-100 (Panel C) libraries were chosen for pairwise comparisons of overlapping TRA and TRB clonotypes. Scatterplots compare fraction of total reads assigned to common clonotypes between replicates.

Cogent NGS Immune Profiler is compatible with rhesus macaque TCR sequencing data

Takara Bio’s Cogent NGS Immune Profiler v1 (CogentIP) performs its TCR-seq read alignment using the human genome as a reference. Here, we validate CogentIP as an appropriate choice for analyzing sequences of rhesus macaque origin.

As verification of species compatibility, we compared the performance of CogentIP to that of another software platform, MiXCR v3. Available on a third-party website, MiXCR v3 can align TCR-seq reads using the rhesus macaque genome as a reference. Using FASTQ files generated from sequencing RM-10 and RM-100 libraries, CogentIP and MiXCR v3 identified similar numbers of TRA and TRB clonotypes (Figure 5, Panel A). As for specific clonotypes identified, there was significant overlap in the RM-10 and RM-100 datasets across both platforms. A comparison of clonotype rankings according to CogentIP and MiCXR v3 found strong correlation between datasets, regardless of RNA input amount. The TCR-seq results from the RM-10 libraries are compared in Figure 5, Panel B.

Figure 5. Cogent NGS Immune Profiler v1 and MiXCR v3 produced similar results when used to analyze TCR-seq data from rhesus macaques. RM-10 and RM-100 libraries created in triplicate from PBMC of three rhesus macaque donors. Full-length TRA and TRB sequences were obtained using the Illumina MiSeq platform. Average reads/sample were 3 million for RM-10 and 1 million for RM-100. CogentIP and MiXCR v3 software were used in parallel to identify clonotypes from the FASTQ files generated from sequencing RM-10 and RM-100 libraries. The total number of TRA and TRB clonotypes across donors is shown in Panel A. Error bars represent the standard deviation among triplicate library preparations. Rankings of matched clonotypes for each TCR chain, as generated by the two platforms, were investigated. A pairwise comparison of TRA and TRB rankings within two of the three replicates from a representative donor’s RM-10 libraries is shown in Panel B.

The distribution of TCR clonotypes identified in the sequencing data can also be depicted visually using chord diagrams. Figure 6 shows examples representing the observed distributions of TRA and TRB V-J segment combinations identified one representative rhesus macaque donor and one human control. All chord diagrams were generated using the CogentIP analysis software. Data input from both species produced visualizations capturing the full spectrum of TRA and TRB V-J pairs.

CogentIP, despite using human genome reference for alignment, can be therefore used with confidence to analyze TCR-seq data from the rhesus macaque.

Figure 6. The full spectrum of TRA and TRB V-J pairs was captured in rhesus macaque and human samples. The RM-100 library of one rhesus macaque donor and in a similar library created using 100 ng of human PBMC RNA are depicted. Each chord diagram depicts the distribution of the indicated TRA and TRB Variable-Joining (V-J) segment combinations. Each arc (on the periphery of each diagram) represents a V or J segment and is scaled lengthwise according to the relative proportion at which the segment is represented in the dataset. Each chord (connecting the arcs) represents a set of clonotypes that include the indicated V-J combination and is weighted according to the relative abundance of that combination in the dataset.

SMARTer Human TCR a/b Profiling Kit generates rhesus macaque TCR sequencing libraries compatible with various Illumina sequencing platforms

A key feature of TCRv2 is compatibility with high-throughput Illumina platforms such as NextSeq® and NovaSeq™. Full-length sequencing on the MiSeq (V3 600 cycle kit) is a great choice for those researchers who want information about the full variable (V) region. Researchers who opt for faster and/or more cost-efficient sequencing may prefer to focus on CDR3 only.

We validated this flexibility using both RM-10 and RM-100 libraries. Mixed TRA/TRB libraries were first run on the MiSeq platform, with full-length sequencing performed at 2 x 300 bp reads. The same libraries were also sequenced using the NextSeq platform for CDR3 sequencing at 2 x 150 bp reads (Figure 7).

The number of clonotypes was strongly correlated between samples, regardless of instrument or sequence length. Therefore, TCR-sequencing libraries from the rhesus macaque produce nearly identical results regardless of the Illumina platform used.

Figure 7. TCRv2 libraries from rhesus macaque samples show highly reproducible clonotype detection, whether sequencing full-length TRA and TRB, or CDR3 regions only. RM-10 and RM-100 libraries were first run on the MiSeq platform, with full-length sequencing of TRA and TRB performed at 2 x 300 bp reads. Average reads/sample were 3 million for RM-10 and 1 million for RM-100. The same libraries and genes were also sequenced using the NextSeq platform for CDR3-region sequencing at 2 x 150 bp reads. Average reads/sample were 5 million for RM-10 and 4 million for RM-100. The total number of TRA and TRB clonotypes detected for each condition in a representative donor is shown. Error bars represent the standard deviation among triplicate library preparations.

Conclusion  

We have shown that the SMARTer Human TCR a/b Profiling Kit v2 (TCRv2) chemistry is compatible with rhesus macaque RNA samples. Resulting libraries are of the same high quality as those created from human samples. The Bioanalyzer traces of TRA/TRB-mixed libraries were similar, regardless of whether the RNA input into TCRv2 came from human or rhesus macaque RNA. Of note, these libraries can be generated without compromise to the many features that make TCRv2 the preferred choice for NGS-based bulk TCR profiling.

The Cogent NGS Immune Profiler v1 software (CogentIP) was validated for use with TCR-sequencing of rhesus macaque samples. When used to process TCR-seq data from rhesus macaques, CogentIP showed reproducibility at low and high inputs. There was an increase in the number of clonotypes identified as RNA input increased. 

Further, we compared data processed with CogentIP to data processed with third-party software, MiXCR v3. While MiXCR v3 allows read alignment with a rhesus macaque reference, CogentIP used a human reference. Nevertheless, CogentIP was able to identify a highly overlapping set of clonotypes between replicates. Additionally, a diverse range of TRA and TRB V-J pairs could be visualized using data input from both species.

Depending on budget and the level of detail desired, researchers can use TCRv2-generated libraries for full-length TRA/TRB sequencing on the MiSeq platform or choose to sequence the CDR3 region only on high-throughput platforms such as NextSeq.

Together, the SMARTer Human TCR a/b Profiling Kit v2 and Cogent NGS Immune Profiler v1 software represent an industry first: a complete TCR repertoire analysis solution for use with the rhesus macaque.

Materials and methods  

Library preparation from two different species

Frozen PBMC from three rhesus macaque donors were purchased from HumanCells Biosciences (Cat. # M5-100-C10M). RNA from PBMCs was extracted using the NucleoSpin RNA kit (Cat. # 740955.50). Human control RNA was included with the SMARTer Human TCR a/b Profiling Kit v2 (Cat. # 634479).

Mixed TRA/TRB libraries were generated using the TCRv2 kit as per the user manual. Briefly, reverse transcription was carried out using an oligo dT with the template-switching TCR SMART UMI Oligo. Next, two rounds of PCR with primers specific for TRA/TRB genes enriched the cDNA with TCR chain sequences. Human and rhesus macaque libraries were prepared in triplicate using 10 ng or 100 ng RNA, amounts chosen according to the upper and lower input range for this kit.

Library quantification and analysis

Following purification and size selection, library yield and size distribution were determined using the Invitrogen Qubit Fluorometer and Agilent 2100 Bioanalyzer instruments, respectively. The Library Quantification Kit (Cat. # 638324) was used to quantify pooled libraries. Libraries were sequenced on both the Illumina MiSeq (600-cycle V3 cartridge; Cat. # MS-102-3003) and Illumina NextSeq (300-cycle v2.5 Mid Output; Cat. # 20024908).

As directed by TCRv2 protocol, sequencing data analysis was performed with Cogent NGS Immune Profiler Software v1 using standard parameters, including the human genome as alignment reference. A parallel analysis was performed with third-party MiXCR v3 software, which allowed for read alignment using a rhesus macaque genome reference obtained from IMGT.

References  

Zhang, Z. et al. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203–14 (2000).

Giudicelli, V. et al. IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic acids res. 34, Database issue D781–4 (2006). 

Thiel, C. et al. Structure and diversity of the T-cell receptor alpha chain in rhesus macaque and chimpanzee. Hum. immunol. 43, 85–94 (1995).

Levinson, G. et al. Sequence and diversity of rhesus monkey T-cell receptor beta chain genes. Immunogenetics 35, 75–88 (1992).

Barennes, P. et al. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat. Biotechnol. 39, 236–245 (2021).

Bolotin, D. A. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380–381 (2015).

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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.

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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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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
634479 SMARTer® Human TCR a/b Profiling Kit v2 48 Rxns USD $4187.00

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 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.

Documents Components Image Data

Back

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.

Back

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.

Back

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.

Back

634479: SMARTer Human TCR a/b Profiling Kit v2

634479: SMARTer Human TCR a/b Profiling Kit v2


Profiling human B-cell receptors with SMART technology

Analyze BCR repertoires from human PBMCs or purified B cells.

Human TCRv2 profiling kit for Illumina sequencing

SMARTer TCR profiling with optimized chemistry, UMIs, UDIs, and bioinformatics support for more accurate, reliable clonotype calling and quantification.

Takara Bio USA, Inc.
United States/Canada: +1.800.662.2566 • Asia Pacific: +1.650.919.7300 • Europe: +33.(0)1.3904.6880 • Japan: +81.(0)77.565.6999
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. © 2025 Takara Bio Inc. All Rights Reserved. All trademarks are the property of Takara Bio Inc. or its affiliate(s) in the U.S. and/or other countries or their respective owners. Certain trademarks may not be registered in all jurisdictions. Additional product, intellectual property, and restricted use information is available at takarabio.com.

Takara Bio

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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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).

Clontech, TaKaRa, cellartis

  • Products
  • COVID-19 research
  • Next-generation sequencing
  • Real-time PCR
  • Stem cell research
  • mRNA and cDNA synthesis
  • PCR
  • Cloning
  • Nucleic acid purification
  • Gene function
  • Protein research
  • Antibodies and ELISA
  • New products
  • Special offers
  • COVID-19 research
  • Viral detection with qPCR
  • SARS-CoV-2 pseudovirus
  • Human ACE2 stable cell line
  • Viral RNA isolation
  • Viral and host sequencing
  • Vaccine development
  • CRISPR screening
  • Drug discovery
  • Immune profiling
  • Publications
  • Next-generation sequencing
  • Spatial omics
  • RNA-seq
  • DNA-seq
  • Single-cell NGS automation
  • Reproductive health
  • Bioinformatics tools
  • Immune profiling
  • Real-time PCR
  • Great value master mixes
  • Signature enzymes
  • High-throughput real-time PCR solutions
  • Detection assays
  • References, standards, and buffers
  • Stem cell research
  • Media, differentiation kits, and matrices
  • Stem cells and stem cell-derived cells
  • mRNA and cDNA synthesis
  • In vitro transcription
  • cDNA synthesis kits
  • Reverse transcriptases
  • RACE kits
  • Purified cDNA & genomic DNA
  • Purified total RNA and mRNA
  • PCR
  • Most popular polymerases
  • High-yield PCR
  • High-fidelity PCR
  • GC rich PCR
  • PCR master mixes
  • Cloning
  • In-Fusion seamless cloning
  • Competent cells
  • Ligation kits
  • Restriction enzymes
  • Nucleic acid purification
  • Automated platforms
  • Plasmid purification kits
  • Genomic DNA purification kits
  • DNA cleanup kits
  • RNA purification kits
  • Gene function
  • Gene editing
  • Viral transduction
  • Fluorescent proteins
  • T-cell transduction and culture
  • Tet-inducible expression systems
  • Transfection reagents
  • Cell biology assays
  • Protein research
  • Purification products
  • Two-hybrid and one-hybrid systems
  • Mass spectrometry reagents
  • Antibodies and ELISA
  • Primary antibodies and ELISAs by research area
  • Fluorescent protein antibodies
  • Services & Support
  • OEM
  • Instrument services
  • Gene and cell therapy manufacturing
  • Customer service
  • Sales
  • Shipping & delivery
  • Technical support
  • Feedback
  • Online tools
  • Partnering & Licensing
  • Vector information
  • OEM
  • Portfolio
  • Process
  • Facilities
  • Request samples
  • FAQs
  • Instrument services
  • Apollo services
  • ICELL8 services
  • SmartChip ND system services
  • Gene and cell therapy manufacturing
  • Services
  • Facilities
  • Our process
  • Resources
  • Sales
  • Make an appointment with your sales rep
  • Online tools
  • GoStix Plus FAQs
  • Vector information
  • Vector document overview
  • Vector document finder
  • Learning centers
  • Automation systems
  • Next-generation sequencing
  • Spatial biology
  • Real-time PCR
  • Nucleic acid purification
  • mRNA and cDNA synthesis
  • PCR
  • Cloning
  • Stem cell research
  • Gene function
  • Protein research
  • Antibodies and ELISA
  • Automation systems
  • Shasta Single Cell System introduction
  • SmartChip Real-Time PCR System introduction
  • ICELL8 introduction
  • Next-generation sequencing
  • RNA-seq
  • Technical notes
  • Technology and application overviews
  • FAQs and tips
  • DNA-seq protocols
  • Bioinformatics resources
  • Webinars
  • Real-time PCR
  • Download qPCR resources
  • Overview
  • Reaction size guidelines
  • Guest webinar: extraction-free SARS-CoV-2 detection
  • Technical notes
  • Nucleic acid purification
  • Nucleic acid extraction webinars
  • Product demonstration videos
  • Product finder
  • Plasmid kit selection guide
  • RNA purification kit finder
  • mRNA and cDNA synthesis
  • mRNA synthesis
  • cDNA synthesis
  • PCR
  • Citations
  • PCR selection guide
  • Technical notes
  • FAQ
  • Cloning
  • Automated In-Fusion Cloning
  • In-Fusion Cloning general information
  • Primer design and other tools
  • In‑Fusion Cloning tips and FAQs
  • Applications and technical notes
  • Stem cell research
  • Overview
  • Protocols
  • Technical notes
  • Gene function
  • Gene editing
  • Viral transduction
  • T-cell transduction and culture
  • Inducible systems
  • Cell biology assays
  • Protein research
  • Capturem technology
  • Antibody immunoprecipitation
  • His-tag purification
  • Other tag purification
  • Expression systems
  • APPLICATIONS
  • Molecular diagnostics
  • mRNA and protein therapeutics
  • Pathogen detection
  • Immunotherapy research
  • Cancer research
  • Alzheimer's disease research
  • Reproductive health technologies
  • Infectious diseases
  • Molecular diagnostics
  • Interview: adapting to change with Takara Bio
  • Applications
  • Solutions
  • Partnering
  • Contact us
  • 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
  • Pathogen detection
  • Sample prep
  • Detection methods
  • Identification and characterization
  • SARS-CoV-2
  • Antibiotic-resistant bacteria
  • Food crop pathogens
  • Waterborne disease outbreaks
  • Viral-induced cancer
  • Immunotherapy research
  • T-cell therapy
  • Antibody therapeutics
  • T-cell receptor profiling
  • TBI initiatives in cancer therapy
  • Cancer research
  • Kickstart your cancer research with long-read sequencing
  • Sample prep from FFPE tissue
  • Sample prep from plasma
  • Cancer biomarker quantification
  • Single cancer cell analysis
  • Cancer transcriptome analysis
  • Cancer genomics and epigenomics
  • HLA typing in cancer
  • Gene editing for cancer therapy/drug discovery
  • Alzheimer's disease research
  • Antibody engineering
  • Sample prep from FFPE tissue
  • Single-cell sequencing
  • Reproductive health technologies
  • Embgenix FAQs
  • Preimplantation genetic testing
  • ESM partnership program
  • ESM Collection Kit forms
  • Infectious diseases
  • Develop vaccines for HIV
  • About
  • BioView blog
  • That's Good Science!
  • Our brands
  • Our history
  • In the news
  • Events
  • Careers
  • Trademarks
  • License statements
  • Quality and compliance
  • HQ-grade reagents
  • International Contacts by Region
  • Need help?
  • Website FAQs
  • BioView blog
  • Automation
  • Cancer research
  • Career spotlights
  • Current events
  • Customer stories
  • Gene editing
  • Research news
  • Single-cell analysis
  • Stem cell research
  • Tips and troubleshooting
  • Women in STEM
  • That's Good Support!
  • About our blog
  • That's Good Science!
  • SMART-Seq Pro Biomarker Discovery Contest
  • DNA extraction educational activity
  • That's Good Science Podcast
  • Season one
  • Season two
  • Season three
  • Events
  • Biomarker discovery events
  • Calendar
  • Conferences
  • Speak with us
  • Careers
  • Company benefits
  • International Contacts by Region
  • United States and Canada
  • China
  • Japan
  • Korea
  • Europe
  • India
  • Affiliates & distributors
  • Need help?
  • Privacy request
Takara Bio
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  • About
  • Contact Us