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DEPArray™ Technology

How does DEPArray™ technology work?

DEPArray™ technology is based on the ability of a non-uniform electric field to exert forces on neutral, polarizable particles, such as cells, that are suspended in a liquid. This electrokinetic principle, called dielectrophoresis (DEP), can be used to gently trap and move cells within DEP “cages.” Silicon Biosystems has leveraged the power of DEP to create the DEPArray™ system, the only automated instrument that can identify, quantify, and recover pure, individual rare cells/cell subpopulations for culture or molecular analysis. For more information, please visit our DEPArray™ technology page.


For what types of applications can DEPArray™ technology be used?

DEPArray™ technology can be used for isolation and recovery of any rare cell type that can be identified by combining positive and negative selection of fluorescent markers and morphological features. The system is ideally suited for any application that would benefit from analysis of individual cells or homogeneous cell populations that are free of contaminants, nonspecific fluorescent particles, and admixtures of cells.

Examples of applications for which DEPArray™ technology is being used include:

  • Analysis of tumor cells and CTCs
  • Identification and validation of fetal cell biomarkers
  • Recovery and analysis of stem cells
  • Cell-cell interaction studies

For more information about applications of DEPArray™ technology, please click here.


How does DEPArray™ technology ensure recovery of pure, single target cells?

Image-based selection ensures that cells that are identified through the multiparametric sorting process are intact, individual cells that meet the selection criteria. The CellBrowser™ software enables visual inspection of cells trapped in the electronic cages, allowing elimination of non-specific fluorescent “events” that might be false positives, cell fragments, or cell clusters.  Recovery of collected cells in a separate, clean buffer solution eliminates impurities and contaminants that could otherwise confound downstream analyses.


How many cells can be processed on the DEPArray™ system?

The DEParray system™ can be used to analyze cell suspensions containing from ten to tens of thousands of cells. Larger cell loads will reduce the ability to achieve single cell resolution. The DEPArray™ system is compatible with commercially available enrichment methods to obtain an optimal cell suspension.


What is the workflow of the DEPArray™ system?

A typical workflow is as follows:

  • A suspension of labeled cells is pipetted into the DEPArray™ cartridge;
  • The array of electrodes is activated to form DEP cages, trapping the labeled cells;
  • The cartridge is scanned in each of the desired fluorescent channels to identify target cells;
  • DEP cages are programmed to move the target cells to a “parking” area;
  • Individual cells or groups of cells are dispensed to the collection vessel of choice.

How are target cells identified and recovered on the DEPArray™ system?

The CellBrowser™ software enables customized configuration of fluorescence channels, allowing users to easily identify one or more specific cell populations of interest. In addition to fluorescence signals, cell perimeter, diameter, and circularity measures are also collected. Image-based selection ensures recovery of intact, individual target cells that exhibit the desired fluorescence patterns and morphological characteristics.


What magnification is available with the camera on the DEPArray™ system?

The system optics provide 10x and 20x magnification with 0.64 and 0.32 micron/pixel resolution, respectively. Images are publication ready and can be exported for use in slides or manuscripts.


What kinds of samples can be analyzed on the DEPArray™ system?

The DEPArray™ system is designed to recover pure cells from a wide range of rare cell suspensions:

  • Live cells
  • Fixed or preserved cells, e.g cells in 2% PFA, cells in CellSave collection tubes
  • Samples with small cell loads, e.g. fine needle aspirates
  • Enriched cells, e.g. cells processed using CellSearch®system
  • Cells labeled with intracellular or extracellular fluorescent probes

Do cells need to be labeled prior to analysis on the DEPArray™ system?

The DEPArray™ system identifies and recovers specific rare cells but does not label or prepare the sample.  The identification of the specific cells of interest and their location within the array is performed using information collected from the camera’s fluorescence channels. Therefore, target cells in the sample do need to be labeled with one or more fluorescent markers in order to properly identify them amongst the background cells in the sample. Information collected using the camera’s bright field, e.g. cell morphology, can be included as an additional selection criteria to define cells of interest.


What fluorescent probes should be used?

Any high-quality fluorescent marker that can be detected in one of the five fluorescent channels available on the DEPArray™ system may be used.  For nuclear staining, DAPI or Hoechst may be used. Hoechst dyes are generally less toxic and exhibit greater cell permeability than DAPI stains. The fluorescent microscopy of the DEPArray™ system is compatible with the labeling used in the CellSearch® system and most conventional FACS-based labeling.


What fluorescent channels are available on the DEPArray™ system?

The DEPArray™ system has 6 optical channels, one of which is configured for bright field analysis.

 

The default fluorescent channels are

 

Fluorochrome

Excitation wavelength (nm)

Emmission wavelength (nm)

DAPI

376

447

FITC

469

510

PE

546

581

APC

616

675

Free

Customizable

Customizable


 In addition to the customizable channel provided, customers may request replacement of one of the default fluorescent channels. Please contact us for more information. 


Do I need to perform an enrichment step prior to putting my sample onto the DEPArray™ system?

For some sample types, no enrichment may be required. When the ratio of target cells to total cell load is low or the total cell load is high an enrichment step may be needed. 


What enrichment methods are compatible with the DEPArray™ system?

The following enrichment methods have been proven compatible by Silicon Biosystems:

  • Veridex CellSearch® System
  • Flow cytometry (FCM, FACS)
  • ScreenCell® filtration devices
  • Ficoll gradient
  • Red blood cell lysis
  • Miltenyi microbeads

For compatibility with other enrichment methods, please contact us.


What kinds of fixatives are compatible with the DEPArray™ system?

Silicon Biosystems has verified that cells fixed in up to 2% PFA and cells preserved in Veridex CellSave collection tubes and processed on the CellSearch® system may be processed on the DEPArray™ system.

 

 For compatibility of cells preserved in other fixatives, please contact us


What kind of downstream analysis can be performed on cells recovered using DEPArray™ technology?

The DEPArray™ system enables isolation of intact, pure cells that are suitable for the most challenging single cell downstream applications, including:

  • Whole genome amplification*
  • Whole genome sequencing
  • Aneuploidy detection
  • Next generation sequencing
  • Mutation and CNV analysis
  • Expression analysis

 *For whole genome amplification optimized for single cells, Silicon Biosystems offers the Ampli1™ WGA Kit.


Can cells recovered using DEPArray™ technology be cultured?

Capture and movement of cells in DEP cages is gentle; cells are not subject to shear force, strain, or potential damage from cell-cell adhesion. Cells can be recovered from the DEPArray™ cartridge directly to cell culture plates with standard cell culture media as the recovery buffer. The viability of recovered cells is dependent on the type of cell and the sample preparation process and time required before recovery by the DEPArray™ system.


Can DEPArray™ technology be used to recover cell clusters?

While we tend to emphasize single pure cell recovery, the DEPArray™ system can be used to recover cell clusters, or microemboli, less than 60 microns.


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