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  • ‹ Back to ICELL8 cx applications
  • Single-cell full-length transcriptome analysis
  • Human TCR profiling and 5' DE
  • Single-cell differential expression analysis
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Home › Products › Next-generation sequencing › Single-cell NGS automation › ICELL8 cx applications › Human TCR profiling and 5' DE

Single-cell NGS automation

  • ICELL8 cx applications
    • Single-cell full-length transcriptome analysis
    • Human TCR profiling and 5' DE
    • Single-cell differential expression analysis
  • ICELL8 applications
    • Single-cell full-length transcriptome analysis
    • Human TCR profiling and 5' DE
    • Single-cell differential expression analysis
    • Single-cell ATAC-seq
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Technical notes View data for this application
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Human TCR profiling and differential expression on the ICELL8 cx system

Single-cell TCR profiling on the ICELL8 cx system

Our high-throughput TCR profiling solution leverages SMART technology (Switching Mechanism At 5' End of RNA Template) and employs a 5' RACE-like approach to capture complete V(D)J variable regions of TCR transcripts from hundreds of single cells isolated on the ICELL8 cx system. As the name suggests, the workflow allows generation of libraries that provide information on both alpha- and beta-chain diversity.

Our high-throughput TCR profiling solution leverages SMART technology (Switching Mechanism at 5' End of RNA Template) and employs a 5' RACE-like approach to capture complete V(D)J variable regions of TCR transcripts from hundreds of single cells isolated on the ICELL8 cx system. As the name suggests, the workflow allows generation of libraries that provide information on both alpha- and beta-chain diversity.

The workflow incorporates Illumina-specific adapter sequences during cDNA amplification for the generation of indexed libraries that are ready for sequencing on Illumina platforms. The application also enables you to perform differential expression analysis by 5' end capture in parallel.

Single T cells isolated with the ICELL8 cx system, as well as positive and negative control samples, are dispensed into a 5,184-nanowell TCR chip that contains preprinted barcodes. Each TCR chip contains 1,728 unique barcodes, and each barcode is printed three times on the chip. Following identification of single-cell-bearing wells using ICELL8 cx CellSelect Software, SMART RT-PCR reagents are dispensed to the wells of samples chosen for further processing. Barcoded cDNAs from the selected wells are PCR-amplified in-chip. The full-length barcoded amplicons are then pooled off-chip, and the purified cDNA is used as template in the first TCR-specific PCR. The product from the first TCR-specific PCR is used as a template in a second TCR-specific PCR to incorporate Illumina indexed primers.

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Cat. # Product Size License Quantity Details
640200 ICELL8® cx TCR Chip 1 Chip USD $1950.00

The ICELL8 cx TCR Chip enables users to analyze T-cell receptor (TCR) diversity from single T cells using the ICELL8 cx Single-Cell System. Each well in the 5,184-nanowell chip contains a preprinted barcode, and 1,728 unique barcodes are present on each chip with each barcode printed in three locations on the chip. ICELL8 cx CellSelect Software is used to detect wells bearing a single cell and direct nanowell-specific delivery of coupled SMART technology RT-PCR reagents to only those wells on the ICELL8 cx TCR Chip that have been selected for further processing. Barcoded cDNA from the selected wells are amplified on-chip by PCR. The full-length barcoded amplicons are then pooled off-chip, and the purified cDNA is used as a template in the first TCR-specific PCR reaction. The product from the first TCR-specific PCR reaction is used as a template in a second TCR-specific PCR reaction to incorporate Illumina indexed primers. Most importantly, the kit allows for efficient, cost-effective, and high-throughput single-cell capture of complete V(D)J variable regions of TCR transcripts.

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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640200: ICELL8 cx TCR Chip

640200: ICELL8 cx TCR Chip
640212 ICELL8® Collection Kit – L Each USD $35.00

The ICELL8 Collection Kit – L consists of a collection fixture, 2.0-ml tubes, and collection film. This kit can be used to spin down a processed ICELL8 chip to collect the contents (e.g., cDNA or library product) of the chip into a tube, when the total extraction volume from the chip will be larger than 0.5 ml.

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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640212: ICELL8 Collection Kit - L

640212: ICELL8 Collection Kit - L
640197 ICELL8® cx Loading Kit Each USD $95.00

The ICELL8 cx Loading Kit includes Blotting Paper along with SmartChip films. This kit supports NGS applications on the ICELL8 cx Single-Cell System.

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

Required Products

Cat. # Product Size Price License Quantity Details
640000 ICELL8® Single-Cell System Each Inquire for Quotation

License Statement

ID Number  
329 This product is protected by one or more of these U.S. Patents 9,132,427, 9,909,171, 9,447,925, 9,951,381 and/or corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
*

The ICELL8 Single-Cell System delivers unparalleled confidence and control for single-cell analysis by enabling precise cell isolation, cell selection, and high sample throughput. The system includes an ICELL8 MultiSample NanoDispenser, a complete imaging system—including microscope, computer, and software—a thermal cycler that accomodates ICELL8 chips, and additional accessories.

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Isolate nuclei and cells of any type

Isolate nuclei and cells of any type

The ICELL8 MSND's large-bore nozzle allows unbiased isolation of any sample. A few of the cell types that have been isolated using the system are listed. For samples highlighted in blue, the ICELL8 Single-Cell System is the first to allow successful isolation of single cells, nuclei, or spheroids.

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Bioanalyzer traces from example TCR libraries

Bioanalyzer traces from example TCR libraries

Electropherogram profiles of TCR sequencing libraries. Electropherograms from three different cell pools (see technical note for more details): Pool 9 (Panel A), 10 (Panel B), and 11 (Panel C). The variation in the profiles reflects the abundance of amplified TCRa (peak at ~900 bp) and TCRb (peak at ~700 bp). Panel D. Positive Control RNA TCR library (generated with 8 x 5 pg Control Jurkat Total RNA). Panel E. Negative Control TCR library shows no library is produced.

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ICELL8 system overview

ICELL8 system overview

Cell dispensing and visualization. After the ICELL8 MutliSample NanoDispenser has dispensed cells into the 5,184-nanowell chip, every well is imaged. Captured images are then processed in the CellSelect software to determine whether wells are empty, contain one cell, or contain multiple cells. This data can then be used to dispense reagents into the single-cell-containing wells.

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640000: ICELL8 Single-Cell System

640000: ICELL8 Single-Cell System
640192 ICELL8® 384-Well Source Plate and Seal Each USD $175.00

The ICELL8 384-Well Source Plate and Seal set is a component of the ICELL8 cx Single-Cell System. It includes NUNC plates and seals for covering the plates, which are utilized for sample and reagent dispense into SmartChip plates for related NGS applications.

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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640192: ICELL8 384-Well Source Plate and Seal

640192: ICELL8 384-Well Source Plate and Seal
640182 ICELL8® Human TCR a/b Profiling Reagent Kit Each USD $499.00

The ICELL8 Human TCR a/b Profiling Reagent Kit is required for the ICELL8 Human TCR a/b Profiling and ICELL8 cx Human TCR a/b Profiling workflows, which enables users to analyze T-cell receptor (TCR) diversity from single T cells using the ICELL8 platform. The kit leverages SMART technology and employs a 5' RACE-like approach to capture complete V(D)J variable regions of TCR transcripts. The reagents are dispensed into a ICELL8 TCR Chip (Cat. No. 640178) or ICELL8 cx TCR Chip (Cat. No. 640200) which includes 5,184 nanowells, containing 1,728 preprinted barcodes (each barcoded is printed three times on the chip) along with primers from the ICELL8 Human TCR a/b Profiling - Indexing Set (Cat. Nos. 640179, 640180 & 640181) that incorporate Illumina-specific adaptor sequences during cDNA amplification. The protocol generates indexed libraries that are ready for sequencing on Illumina platforms. The protocol also allows whole transcriptome library generation of 5' ends of all transcripts.

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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640182: ICELL8 Human TCR a/b Profiling Reagent Kit

640182: ICELL8 Human TCR a/b Profiling Reagent Kit
640179 ICELL8® Human TCR a/b Profiling - Indexing Primer Set 1 Chip USD $198.00

The ICELL8 Human TCR a/b Profiling - Indexing Primer Set contains PCR primers for the amplification of indexed, paired-end, Illumina-compatible sequencing libraries.

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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640179: ICELL8 Human TCR a/b Profiling - Indexing Primer Set

640179: ICELL8 Human TCR a/b Profiling - Indexing Primer Set
640180 ICELL8® Human TCR a/b Profiling - Indexing Primer Set 5 Chips USD $648.00

The ICELL8 Human TCR a/b Profiling - Indexing Primer Set contains PCR primers for the amplification of indexed, paired-end, Illumina-compatible sequencing libraries.

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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640180: ICELL8 Human TCR a/b Profiling - Indexing Primer Set

640180: ICELL8 Human TCR a/b Profiling - Indexing Primer Set
640181 ICELL8® Human TCR a/b Profiling - Indexing Primer Set 10 Chip USD $1250.00

The ICELL8 Human TCR a/b Profiling - Indexing Primer Set contains PCR primers for the amplification of indexed, paired-end, Illumina-compatible sequencing libraries.

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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640181: ICELL8 Human TCR a/b Profiling - Indexing Primer Set

640181: ICELL8 Human TCR a/b Profiling - Indexing Primer Set
635011 SMARTer-Seq™ Magnetic Separator - PCR Strip Each USD $205.00

The SMARTer-Seq Magnetic Separator - PCR Strip is designed especially for separation of magnetic beads (like AMPure XP beads; Beckman Coulter), from solution. This stand holds up to 24 0.2-ml PCR tubes in two rows, and is designed for capture of magnetic beads in 10–20 minutes. It is ideally suited for magnetic bead-based DNA purification and size selection techniques as used with most of our products for next-generation sequencing.

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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635011: SMARTer-Seq Magnetic Separator - PCR Strip

635011: SMARTer-Seq Magnetic Separator - PCR Strip

ICELL8 cx TCR profiling workflow ICELL8 cx TCR Profiling User Manual
Combined 5' differential expression and TCR profiling tech note TCR profiling plus 5’ DE tech note
Process your ICELL8 single-cell TCR a/b output ICELL8 scTCR Analyzer software

Overview

  • Sensitivity—RACE-based approach allows for the detection of low-abundance TCR variants
  • Specificity—Full length reads, with majority of reads on target and accurate pairing information
  • Differential expression by 5' sequence enrichment—generate differential expression data for all transcripts by mapping the 5' ends
  • Flexible, high-throughput single-cell analysis—generate sequencing data from hundreds of single cells in parallel and analyze cells from up to eight different samples in a single experiment

More Information

Applications

  • Human TCR repertoire analysis in single cells (TCRα and TCRβ clonotypes)
  • Differential expression by 5' end capture

Components

The following items are required to complete the workflow:

ICELL8 cx Single-Cell System (Cat. # 640188 & Cat. # 640189)
Cat. # Product 1 item required per:
640182 ICELL8 Human TCR a/b Profiling Reagent Kit 1 chip
640179 ICELL8 Human TCR a/b Profiling - Indexing Primer Set* 1 chip
640180 ICELL8 Human TCR a/b Profiling - Indexing Primer Set* 5 chips
640181 ICELL8 Human TCR a/b Profiling - Indexing Primer Set* 10 chips
640200 ICELL8 cx TCR Chip 1 run
640212 ICELL8 Collection Kit – L 1 chip
640197 ICELL8 cx Loading Kit 1 chip
640192 ICELL8 384-Well Source Plate and Seal (5/pack) 1 chip
740609.50 NucleoSpin Gel and PCR Clean-Up 1 chip
635011 SMARTer-Seq Magnetic Separator - PCR Strip (or equivalent) Reusable

*Note: Cat. No. 640179 contains enough primers for one chip. If you plan on processing multiple chips at a time, please purchase the appropriate indexing primer set. Cat. No. 640180 has indexing primers for up to five chips, while Cat. No. 640181 has primers for up to 10 chips.

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.


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