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cDNA Synthesis & Library Construction

Products >  cDNA_Synthesis_and_Library_Construction >  NGS_Automation >  Single-Cell_Automation >  Single-Cell_Automation_Overview

Single-Cell Automation Overview

Open platform for single-cell analysis

High-throughput single-cell isolation, selection, and processing

  • Be in control—selectively process only the cells of choice
  • Be more confident in your data—reduce batch effects and the unnecessary analysis of empty or multi‑cell wells

Jump to: SMART-Seq technology | TCR profiling | Flexible cell-size isolation

Overview of dispensing and imaging
Cell dispensing and visualization. After the ICELL8 MutliSample NanoDispenser (MSND) 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.

Overview of system

Dispensing Imaging
  • Automated dispensing of cells and reagents by the ICELL8 MSND
  • Accommodates up to eight samples
  • Flexible options for volume and pattern dispensation
  • Unbiased isolation of 1,000–1,800 single cells in a 5,184-nanowell chip
  • Automated rapid and robust imaging with the ICELL8 Imaging Station
  • Simple user interface
  • Imaging channels for live/dead analysis of cells*

*CellTracker Red or a combination of Hoechst and propidium iodide dyes can be used for cell identification and viability assessment.

Selection Chips and reagents (sold separately)
  • Autoselect single cells or nuclei for downstream analysis with CellSelect software
  • Evaluate staining for cell viability
  • Distinguish single‑cell‑containing wells from empty and doublet-containing wells
  • 5,184-nanowell chips
  • Chips of varying depth hold 150, 250, or 350 nl
  • Blank chips and preprinted chips for specific applications

Gain clarity from complex samples

To address cellular heterogeneity, researchers need an unbiased method to analyze large numbers of single cells, more control over selection of the isolated cells to accelerate downstream processing, and the flexibility to analyze multiple parameters per experiment. The SMARTer ICELL8 Single-Cell System meets these requirements with an integrated and automated platform.

By rapidly isolating and characterizing hundreds of rare and unique cells, you can look beyond the aggregate signal seen with traditional bulk processing. The statistical inferences possible with the SMARTer ICELL8 system greatly expand the opportunities for discovery within any biological system.

Full-length transcriptome analysis

Bringing the unparalleled sensitivity of SMART-Seq technology to the SMARTer ICELL8 Single-Cell System generates high-quality RNA-seq data from hundreds of single cells. Libraries prepared using this system have a high number of transcripts and genes, even at low sequencing depths. Furthermore, the library complexities remain similar even upon downsampling. Download our application note on full-length single-cell RNA-seq using the SMARTer ICELL8 system.

High-quality, full-length transcriptome analysis

TCR profiling

Combining the SMARTer ICELL8 system with a 5′-RACE-like approach and SMART technology for next-generation sequencing library preparation allows the capture of the full-length variable regions of TCR-α and -β chains for hundreds of cells. Download our application note on high-throughput single-cell TCR profiling using the SMARTer ICELL8 system.

TCR clonotype determination

Cell size flexibility

Unbiased cell-size isolation
The SMARTer ICELL8 system provides the flexibility of working with both large and small cell types, including nuclei. Above images are of adult cardiomyocytes dispensed in the nanowells. Cells are stained with Hoechst and propidium iodide. Data kindly provided by Dr. Stefan Günther, Max Planck Institute.

Isolate cells of any size

Cell line/typeSpeciesSource
BaF/3MousePre-B cells
Primary cellsMouseBone marrow
Primary cellsMouseCardiomyocyte (adult)
ESC; Differentiated ESCMouseEmbryonic stem cells
EarMouseInner ear organs
Primary cellsMouseEmbryos
FACS-sorted lymphocytesHumanBone marrow
Fetal cortexHumanPrimary cells
Fetal neuronsHumanFetal brain
Gut cellsMosquitoGut
HCT 116HumanColon
HSPCMouseHematopoietic stem cells
KU812HumanBlood, CML myeloblast
Lung epitheliaMousePrimary FACS-sorted cells
MDA-MB-231HumanMammary gland
MIA PaCa-2HumanPancreas
Nasal epitheliaHumanPrimary nasal scraping
NeuronsMouseFresh dissection
NucleiHumanFrozen lung tumor;
frozen breast cancer
Planaria SCPlanariumStem cells
RetinaMousePrimary cells
Scheider S2DrosophilaEmbryo
U-87-MGHumanGlioblastoma; astrocytoma
UTHSCHumanBone marrow EW-8 Ewing
Z-138HumanB-cell lymphoma

Table I. 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 SMARTer ICELL8 Single-Cell System is the first to allow successful isolation of single cells, nuclei, or spheroids.

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