Takara SMART-Seq Human TCR (with UMIs)

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 (listed below) does not in any way impact the protocols or functional performance of these kits.

For added flexibility, indexes are not included in the kit, but a choice of indexing primers is sold separately (see Unique Dual Index [UDI] kits)

SMART-Seq Human TCR (with UMIs) is powered by robust chemistry that provides unparalleled sensitivity and reproducibility. The kit leverages SMART (Switching Mechanism at 5end of **R**NA **T**emplate) full-length cDNA synthesis technology and pairs NGS with a 5-RACE approach to capture the complete V(D)J variable regions of human TRA and TRB genes.

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 (listed below) does not in any way impact the protocols or functional performance of these kits.

For added flexibility, indexes are not included in the kit, but a choice of indexing primers is sold separately (see Unique Dual Index [UDI] kits)

SMART-Seq Human TCR (with UMIs) is powered by robust chemistry that provides unparalleled sensitivity and reproducibility. The kit leverages SMART (Switching Mechanism at 5end of **R**NA **T**emplate) full-length cDNA synthesis technology and pairs NGS with a 5-RACE approach to capture the complete V(D)J variable regions of human TRA and TRB genes.

The kit is designed to work with a range of RNA input amounts (RIN ≥8; depending on the sample type) and has been shown to yield high-quality sequencing libraries from as little as 10 ng to 1 µg of total RNA obtained from peripheral blood leukocytes, 20 ng to 200 ng of total RNA obtained from whole blood, 1 ng to 100 ng of total RNA obtained from T cells, or from 1,000 to 10,000 purified, whole T cells. Libraries can be generated to obtain both alpha and beta chain diversity information. This latest profiling kit also includes unique molecular identifiers (UMI), making it possible to remove reads derived from PCR duplicates and sequencing errors, thus ensuring more accurate and reliable results. Generate up to 384 multiplexed Illumina libraries using the Unique Dual Index kits (Cat. Nos. 634752–634756; sold separately).

As a part of a complete solution, analyze your sequencing data with our free-to-use Cogent NGS Immune Profiler Software (Cogent IP). This software enables high-quality TCR profiling analysis, including count and identification of clonotypes and sequence information for V(D)J regions. As a bonus, our cloud-based Cogent NGS Immune Viewer allows you to quickly and easily visualize and produce publication-quality tabulated outputs and figures of your data using output files from Cogent IP.

Benefits of this kit include:

• Use of UMIs to correct for PCR and sequencing errors
• Compatibility with UDIs, allowing for greater confidence in sequencing on a patterned flow cell (such as the NovaSeq™ system) and the ability to pool a greater number of samples
• Flexibility to sequence on any Illumina instrument
• Full-length V(D)J analysis or CDR3-only analysis
• Access to Cogent NGS Immune Profiler Software and Immune Viewer Software, an easy-to-use analysis pipeline for users of any bioinformatic experience level, for faster data analysis

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Overview

• Compatible with a wide range of sample inputs: 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 from T cells) or purified, whole T cells (1,000 to 10,000 cells)
• Simple PCR amplification: a single primer pair for each TCR (alpha or beta) subunit per reaction
• UMI-based correction: removal of reads derived from PCR duplicates and sequencing errors
• Sensitive and specific clonotype detection: optimized cDNA library generation
• UDI implementation: increased multiplexing and confidence for sequencing on high-throughput sequencers
• Illumina-ready sequencing libraries: Illumina-compatible index sequences are incorporated for multiplexing up to 384 libraries in a single run
• Flexible sequencing options: either full-length V(D)J information on the MiSeq™ system or CDR3 information on all Illumina platforms
• Complete workflow: robust chemistry complemented with use of our Cogent NGS Immune Profiler Software and web-based Cogent Immune Viewer* for sequencing data analysis and visualization
  _*The Cogent NGS Software tools are free to use with this kit for both academic and for-profit entities
  _

Figure 1. Sensitive and reproducible clonotype detection from a broad range of RNA amounts. TRA and TRB libraries were generated from 1, 10, and 100 ng of human CD3+ T-cell total RNA and 1,000 and 10,000 CD3+ T cells. The sequence reads were processed by the Cogent NGS Immune Profiler Software.

% Jurkat RNA spiked in to 100 ng of PBMC RNA	Total read count (TRA/TRB)	Without UMI collapse			With UMI collapse
# of TRB raw reads	# of reads for TRBV12‑3-TRBJ1‑2	Detected percentage of Jurkat reads	# of detected UMIs	# of UMIs for TRBV12‑3-TRBJ1‑2	Detected percentage of Jurkat UMIs
---	---	---	---	---	---	---	---
10.0%	2,500,000	1,565,005	397,179	25.0%	281,280	62,629	22.0%
1.0%	2,500,000	1,422,102	47,160	3.3%	219,776	6,426	2.9%
0.1%	2,500,000	1,366,127	5,412	0.4%	189,580	631	0.33%
0.01%	2,500,000	1,218,025	521	0.043%	196,615	74	0.038%
0.001%	2,500,000	1,331,465	909	0.068%	197,870	6	0.003%
0.0001%	2,500,000	1,409,199	-	0%	124,149	-	0%
0%	2,500,000	1,222,245	-	0%	197,933	-	0%

Table 1. Assessing the sensitivity and reproducibility of the SMART-Seq approach. Spike-in analysis was performed in replicate on PBMC RNA samples spiked at varying concentrations (10%, 1%, 0.1%, 0.01%, 0.001%, and 0.0001%) with RNA obtained from a homogeneous population of leukemic Jurkat T cells (containing TRBV12-3-TRBJ1-2 clonotypes). TRB CDR3 regions were amplified from 100 ng of total RNA using the SMARTer Human TCR a/b Profiling Kit v2 (TCRv2) and sequenced. Reads of 2 x 150 bp were obtained on an Illumina NextSeq® system. The sequencing reads were downsampled to 2.5 M reads. Read results for spike-in concentrations identified as the reliable concentration limit for each criterion (without and with UMI collapse) have data highlighted in gray. Without UMI collapse, PCR duplicates of TRBV12-3 were observed in 0.0010% of the raw reads.

Figure 2. Superior sensitivity and reproducibility. We split 5 M PBMC cells from two different healthy donors for RNA and gDNA extraction. 1.6 µg of gDNA was used for library preparation according to the manufacturers instructions (15% of the total amount of extracted gDNA). 100 ng of RNA was used for library preparation (2% of the total amount of extracted RNA). Clonotype numbers for _TCRa/b_ libraries are shown from each company (NT: not tested). In the comparison, the Takara Bio TCR profiling kit generated an average of 48.7K and 163K clonotypes for _TRA_ and _TRB,_ respectively, representing a 290% increase against Company Qs RNA-based approach and a 145% increase against Company A`s gDNA-based approach. Importantly, the RNA methods used only 2% of the total RNA from the 5 M PBMCs.

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Applications

Human TCR repertoire analysis (TCRα and TCRβ subunits)

Additional product information

Please see the product`s Certificate of Analysis for information about storage conditions, product components, and technical specifications. Please see the Kit Components List to determine kit components. Certificates of Analysis and Kit Components Lists are located under the Documents tab.