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  • 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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Home › Products › Next-generation sequencing › Single-cell NGS automation › ICELL8 applications › Single-cell differential expression analysis

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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Differential expression analysis on the ICELL8 Single-Cell System

NGS 3' DE workflow

By leveraging Takara Bio's expertise in single-cell RNA-seq library construction and the cell isolation and selection capabilities of the ICELL8 platform, the ICELL8 3' DE and ICELL8 3' DE for UMI workflows enable high-throughput preparation of Illumina libraries for differential expression analysis of single cells from up to eight different samples in parallel.

By leveraging Takara Bio's expertise in single-cell RNA-seq library construction and the cell isolation and selection capabilities of ICELL8 systems, the ICELL8 3' DE and ICELL8 3' DE for UMI workflows enable high-throughput preparation of Illumina libraries for differential expression analysis of single cells from up to eight different samples in parallel.

The ICELL8 Chip and Reagent 3' DE Kit (Cat. # 640164, 640165, 640166) is compatible with the original ICELL8 Single-Cell System. Included in the kit are an ICELL8 3' DE Chip (Cat. # 640143), a 5,184-nanowell SmartChip that contains preprinted oligo(dT) primers, and reagents for cDNA synthesis and Illumina library prep.

Following staining and dilution, sample cells are dispensed into chip nanowells using the ICELL8 MultiSample NanoDispenser (MSND). Wells containing single, viable cells are selected using the ICELL8 Imaging System and the CellSelect Software provided with the ICELL8 system. Following the selection of cells for processing and analysis, RT-PCR reagents are dispensed into the corresponding wells, and cDNA synthesis and amplification are performed in-chip in a single run. Following RT-PCR, cDNA products are pooled and purified, and sequencing libraries are prepared using a transposase-based method that enriches for cDNA derived from mRNA 3' ends, followed by a limited-cycle PCR amplification step that incorporates Illumina index sequences.

Sequencing data from the resulting libraries can be traced back to individual cells using the nanowell-specific barcode sequences and can be used to perform differential gene expression analysis by mRNA 3' end-counting. By yielding high-quality, 3'-focused sequencing data from hundreds of cells in parallel, these kits provide an efficient, cost-effective solution for high-throughput differential expression analysis of single cells.

The ICELL8 3' DE for UMI Reagent Kit is used with the ICELL8 3' DE Chip as part of the ICELL8 3' DE with UMI workflow, which enables Illumina sequencing and differential gene expression analysis-via transcript 3' end counting-of single cells isolated on the ICELL8 system.

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Cat. # Product Size License Quantity Details
640048 ICELL8® Collection Kit 1 Pkg USD $27.00

The ICELL8 Collection Kit consists of a fixture, tube, and film that allow users to spin down the contents of an ICELL8 chip to collect the contents of processed chips (e.g., extracted cDNA) into a tube.

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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640048: ICELL8 Collection Kit

640048: ICELL8 Collection Kit

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
640109 ICELL8® Loading Kit 1 Pkg USD $27.00

The ICELL8 Loading Kit contains films and blotting paper designed to be used with ICELL8 chips. The Blotting Paper is used to blot chips after dispensing of cells into a chip by the ICELL8 MultiSample NanoDispenser (MSND). The Optical Imaging Film is used to seal chips prior to imaging of the nanonwells with the ICELL8 Imaging System. The TE Sealing Film is used to seal the chip after reagents have been dispensed into cells selected for processing for reverse transcription.

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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640109: ICELL8 Loading Kit

640109: ICELL8 Loading Kit
640018 MSND 384-Well Source Plate and Seals (430-000025) 20/Pack USD $482.00

20 Pack of MSND 384-Well Source Plate and Seals. Formerly 430-000025.

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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640018: MSND 384-Well Source Plate and Seals (430-000025)

640018: MSND 384-Well Source Plate and Seals (430-000025)
640037 MSND 384-well Source Plate and Seals (430-000258) 120/Pack USD $1782.00

120 pack of MSND 384-well Source Plate and Seals. Formerly 430-000258.

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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640037: MSND 384-well Source Plate and Seals (430-000258)

640037: MSND 384-well Source Plate and Seals (430-000258)

ICELL8 3' DE UM ICELL8 Chip and Reagent 3' DE Kit User Manual
ICELL8 3' DE for UMI UM ICELL8 3' DE for UMI Reagent Kit User Manual

Overview

  • High-throughput single-cell analysis—generate sequencing data from hundreds of single cells in parallel
  • Sample flexibility—analyze cells from up to eight different samples in a single experiment
  • mRNA 3' sequence enrichment—reduce the number of reads required for differential gene expression analysis by enriching for sequences derived from mRNA 3' ends
  • Reduced sample handling—minimize variability with automated cell isolation and selection, and sample pooling prior to library construction
  • Illumina sequencing libraries—generate libraries suitable for sequencing on all Illumina platforms

NOTE: The procedures for each 3' DE kit vary, so be sure to reference the appropriate user manual.

More Information

Components

The following items are required to complete the workflow:

ICELL8 3′ DE workflow
Cat. # Product 1 item required per:
640167 ICELL8 3' DE Reagent Kit 1 chip
640143 ICELL8 3' DE Chip 1 run
640048 ICELL8 Collection Kit 1 chip
640109 ICELL8 Loading Kit 1 chip
640018 MSND 384-Well Source Plate and Seals* (20/pack) 10 chips
640037 MSND 384-Well Source Plate and Seals* (120/pack) 60 chips
Other available kit packages that include chip(s), reagent kit, loading kit, and collection kit
640164 ICELL8 Chip and Reagent 3' DE Kit 1 chip (contained in kit)
640165 ICELL8 Chip and Reagent 3' DE Kit 3 chips (contained in kit)
640166 ICELL8 Chip and Reagent 3' DE Kit 5 chips (contained in kit)

ICELL8 3′ DE for UMI workflow
Cat. # Product 1 item required per:
640005 ICELL8 3' DE for UMI Reagent Kit 1 chip
640143 ICELL8 3' DE Chip 1 run
640048 ICELL8 Collection Kit 1 chip
640109 ICELL8 Loading Kit 1 chip
640018 MSND 384-Well Source Plate and Seals* (20/pack) 10 chips
640037 MSND 384-Well Source Plate and Seals* (120/pack) 60 chips

*Note: Cat. No. 640018 contains enough plates and film for 10 chips. If you plan on processing more chips, Cat. No. 640037 has enough plates and sealing film for up to 60 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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Comparing single-cell RNA-seq on automation platforms

Which systems should you trust with your single-cell RNA-seq experiments? This blog post discusses a comprehensive study performed by the Association of Biomolecular Resource Facilities (ABRF) Genomics Research Group (GRG), in which the performance of automated, single-cell NGS platforms from several providers were compared in head-to-head experiments. The ICELL8 Single Cell System with 3' (DE) expression profiling excelled in important data-quality metrics, including sensitivity, read efficiency, and gene diversity.

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  • High-throughput qPCR solutions
  • RNA extraction and analysis for real-time qPCR
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  • Single-cell cloning of edited hiPS cells
  • mRNA and cDNA synthesis
  • In vitro transcription
  • cDNA synthesis kits
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  • Purified total RNA and mRNA
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  • High-yield PCR
  • High-fidelity PCR
  • GC rich PCR
  • PCR master mixes
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  • In-Fusion seamless cloning
  • Competent cells
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