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  • ‹ Back to ICELL8 applications
  • Single-cell full-length transcriptome analysis
  • Human TCR profiling and 5' DE
  • Single-cell differential expression analysis
  • Single-cell ATAC-seq
Overviews ICELL8 learning resources
ICELL8 consumables product page ICELL8 consumables
Citations ICELL8 citations (including scATAC-Seq)
Home › Products › Next-generation sequencing › Single-cell NGS automation › ICELL8 applications › Single-cell ATAC-seq

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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Overviews ICELL8 learning resources
ICELL8 consumables product page ICELL8 consumables
Citations ICELL8 citations (including scATAC-Seq)

Single-cell ATAC-seq

Buy products for scATAC-seq using ICELL8 technology

Epigenomic information provides greater insight into gene regulation, but is complicated by the fact that individual cells (even those of the same type) may have distinct epigenomes. Our ICELL8 platform offers a high-throughput solution that enables the generation of single-cell ATAC-seq (scATAC-seq) libraries from >1,000 cells in a 4–5-hour on-chip automated workflow.

Epigenomic information provides greater insight into gene regulation, but is complicated by the fact that individual cells (even those of the same type) may have distinct epigenomes. Our ICELL8 platform offers a high-throughput solution that enables the generation of single-cell ATAC-seq (scATAC-seq) libraries from >1,000 cells in a 4–5-hour on-chip automated workflow.

ATAC-seq: generate genome-wide chromatin accessibility maps

ATAC-seq stands for Assay for Transposase-Accessible Chromatin using sequencing. ATAC-seq is used for the genome-wide mapping of chromatin accessibility and employs a hyperactive Tn5 transposase to selectively insert DNA adapters into accessible chromatin loci. Adapter-ligated DNA fragments are then amplified by PCR and used to generate sequencing-ready libraries. This method represents a powerful tool for investigating the dynamics of gene expression regulation and allows for the simultaneous examination of the accessibility of genomic DNA to transcription factors and nucleosome position(s) in regulatory sites, while providing a genome-wide map of chromatin accessibility.

ATAC-seq on the ICELL8 platform

Our ICELL8 platform enables a simple, relatively inexpensive scATAC-seq workflow that offers a 20-fold increase in throughput compared to prior methods. Our technology allows the generation of ATAC-seq data from >1,000 viable cells isolated and selected automatically with the ICELL8 Single-Cell System (Cat. No. 640000) and CellSelect Software. The chip is then transferred to the ICELL8 Chip Cycler where tagmentation, indexing, and PCR amplification is performed on-chip. Following amplification, full-length amplicons are pooled off-chip, purified, and the purified cDNA is amplified to yield the final sequencing-ready libraries.

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Cat. # Product Size License Quantity Details
640183 ICELL8® 250v Chip 1 Chip USD $698.00

The ICELL8 250v Chip is a 250-nl volume, V-bottom chip that enables users to dispense and image cells using the ICELL8 Single-Cell System. All wells in the 5,184-nanowell chip are unprinted and have a maximum working volume of 250 nl and a depth of 1.600 mm. Cells of choice are diluted, as per the appropriate application-specific ICELL8 user manual, and then dispensed and/or imaged on the ICELL8 system. CellSelect Software is used to image and detect single-cell-bearing wells.

The ICELL8 250v Chip is used in the SMART-Seq ICELL8 application kit protocol along with the SMART-Seq ICELL8 Reagent Kit, which enables users to analyze full-length transcripts using the ICELL8 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.

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640183: ICELL8 250v Chip

640183: ICELL8 250v Chip
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
640196 ICELL8® Blank Chip Reagent Kit Each USD $102.00

The ICELL8 Blank Chip Reagent Kit includes ICELL8 Fiducial Mix and Second Diluent to support NGS applications on the ICELL8 cx Single-Cell System or ICELL8 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.

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640196: ICELL8 Blank Chip Reagent Kit

640196: ICELL8 Blank Chip Reagent Kit
RF001A e2TAK® DNA Polymerase 200 Rxns USD $73.00

e2TAK can be substituted for standard Taq DNA Polymerase in a variety of general PCR experiments, providing improved efficiency and performance at reduced cost.

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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Amplification of a 2 kb lambda-DNA Fragment with e2TAK DNA Polymerase and Company P's DNA Polymerase

Amplification of a 2 kb lambda-DNA Fragment with e2TAK DNA Polymerase and Company P's DNA Polymerase
Amplification of a 2 kb lambda-DNA Fragment with e2TAK DNA Polymerase and Company P's DNA Polymerase. Excellent sensitivity and yield are observed when amplifying a 2 kb lambda fragment. Lane 1: No template; Lane 2: 100 fg; Lane 3: 1 pg; Lane 4: 10 pg; Lane 5: 100 pg; Lane M: lambda-Hind III digest.

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Amplification of Various Size DNA Fragments using e2TAK DNA Polymerase and Three Other Competitors' enzymes

Amplification of Various Size DNA Fragments using e2TAK DNA Polymerase and Three Other Competitors' enzymes
Amplification of Various Size DNA Fragments using e2TAK DNA Polymerase and Three Other Competitors' enzymes.

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RF001A: e2TAK DNA Polymerase

RF001A: e2TAK DNA Polymerase
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)
639132 Advantage® UltraPure dNTP Combination Kit (100 mM each dNTP) 250 uL/dNTP USD $340.00

Advantage UltraPure dNTP Combination Kit contains all four dNTPs in aqueous solution in separate tubes. All four dNTPs are ready for use in PCR amplification, cDNA synthesis, labeling reactions, dideoxy sequencing, and in vitro mutagenesis.

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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639132: Advantage UltraPure dNTP Combination Kit (100 mM each dNTP)

639132: Advantage UltraPure dNTP Combination Kit (100 mM each dNTP)
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)

Protocols ICELL8 scATAC-seq protocol
Technical note scATAC-Seq tech note
Featured kits ATAC-Seq required reagents

Overview

  • High library complexity—more than 13,000 unique fragments per single cell
  • Good signal-to-noise ratio—greater than 10-fold enrichment of desired reads at transcriptional start sites
  • Robust clustering—application data with PBMCs demonstrates robust clustering of B, T, and monocyte cells

More Information

Applications

  • High-throughput scATAC-seq library generation for Illumina platforms
  • Nucleosome mapping
  • Determination of transcription factor occupancy

Components

The following items are required to complete the workflow:

ICELL8 Single-Cell System (Cat. # 640000)
Cat. # Product 1 item required per:
640196 ICELL8 Blank Chip Reagent Kit 1 chip
640183 ICELL8 250v Chip 1 run
640048 ICELL8 Collection Kit 1 chip
640018 MSND 384-Well Source Plate and Seals* (20/pack) 4 chips
640037 MSND 384-Well Source Plate and Seals* (120/pack) 24 chips
Additional Takara Bio reagents required for the protocol:
RF001A e2TAK DNA Polymerase
639132 Advantage UltraPure dNTP Combination Kit (100 mM each dNTP)

*Note: Cat. No. 640018 contains enough plates and film for 4 chips. If you plan on processing more chips, Cat. No. 640037 has enough plates and sealing film for up to 24 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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Overview ICELL8 technology overview
ICELL8 cx tech specs ICELL8 cx technical specs
ICELL8 cell types isolated ICELL8 cell isolation list
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