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For accessible, affordable and reliable recovery
of viable single cells
  • Works in conjunction with inverted microscopes
  • Microscope compatibility testing available in the demo tool
  • Ideal for a variety of eukaryotic cells
  • Cell viability and purity maintained after isolation
  • Isolated cells suitable for use in various single-cell workflows

The QIAscout device together with its core technology, the QIAscout 12,000-Microraft Array, simplifies single-cell isolation while providing cells with a suitable environment similar to a standard cell culture dish. Whether you are performing single-cell sequencing, whole genome and transcriptome amplification or single-cell miRNA analysis; all you need to get started is your cell sample, the QIAscout device and an inverted microscope. The single cells isolated with the QIAscout can be combined with QIAGEN’s single-cell kits for your direct analysis or used for clonal expansion.

Explore the virtual demo to learn more about the QIAscout, see how easy it is to setup and start working, and find a guide to compatible microscopes and objectives.

Explore Virtual Demo

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Cat No./ID: 9002730
QIAscout Instrument
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The QIAscout instrument platform comprises a controller, power supply for controller, a magnetic collection plate, a motorized release device, 4 inserts for release device, protective lid for release device and a magnetic wand. The instrument can only work in conjunction with the QIAscout arrays.
Cat No./ID: 9002733
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The QIAscout consists of the QIAscout instrument platform comprising a controller, power supply for controller, a magnetic collection plate, a motorized release device, 4 inserts for release device, protective lid for release device and a magnetic wand as well as a starter pack of 5 QIAscout 12,000-Microraft Arrays
Cat No./ID: 928031
QIAscout 12,000-Microraft Arrays (5)
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A starter pack of 5 arrays to be used with the QIAscout instrument platform
The QIAscout is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

PCA analysis of miRNA expression of single cells.
Differential response in miRNA expression amongst treated single cells with 3 distinct populations.
No DNA contamination observed with the release needle in qPCR analysis.
A qPCR amplification plots of 15 microrafts pierced using unwashed release needle. B qPCR amplification plots of negative controls (water). C qPCR amplification plots of positive controls (10 ng DNA) showing a CT value of 27.
No cell contamination observed with the magnetic wand in Pyrosequencing analysis.
A Representative pyrogram showing the G>A point mutation in the human EGFR gene in a sample with single SW48 cells (positive control). B Representative pyrogram showing absence of the A allele in single HT-29 cells, transferred with the same unwashed magnetic wand as the SW48 cells. C Frequency of the A allele in two pierced HT-29 cells (negative control), two pierced SW48 cells (positive control) and 24 pierced HT-29 cells. Single SW48 cells transferred using a clean magnetic wand (positive control) show a mean frequency of A allele (=point mutation) of 50.7%. Pierced single HT-29 cells transferred using an unwashed magnetic wand and analyzed for the presence of SW48 cell contamination showed a similar frequency of A allele when compared to the pierced single HT-29 cells transferred using the clean magnetic wand (negative control), indicating no contamination between the two cell lines, the arrays and the microrafts.
Highly viable single-cell isolation

Cells remain viable for several days and form subpopulations, irrespective of whether the pierced microrafts containing single cells are transferred to a cell culture dish or single cells present on microrafts are left intact and allowed to grow on the QIAscout array itself (see corresponding Application Note titled “Rapid and Efficient Method of Isolation and Recovery of Highly Viable Single Cells Free of Contamination” under the “Product Resources” tab).

Highly pure single-cell isolation

The release needle and the magnetic wand do not act as sources of contamination while isolating single cells using the QIAscout. This was verified using two approaches, qPCR (see Figure “No DNA contamination observed with the release needle in qPCR analysis”) and Pyrosequencing (see Figure “No cell contamination observed with the magnetic wand in Pyrosequencing analysis”), after processing cells using the REPLI-g Single Cell Kit.

Highly targeted single-cell isolation

The QIAscout method allows efficient and reliable isolation of single targeted cells. Selection of cells can be based on different cellular parameters like cell morphology or fluorescence. Conventional manual methods like pipetting and serial dilution are less successful in selective isolation of single cells when compared to the novel QIAscout technology (data not shown).

Unique miRNA expression profiling from single cells

The precise and affordable single-cell isolation technology in combination with miScript Single Cell qPCR Kit and miScript miRNA PCR Array facilitates the downstream expression analysis of miRNAs from individual cells. In bulk cell analysis “cellular averages” mask intrinsic transcriptional variability across individual cell subpopulations. Distinct cell populations can be effectively revealed by single-cell analysis using the QIAscout for miRNA expression profiling (see Figure “Principle Component Analysis (PCA) of miRNA expression of single cells”).
The QIAscout system is an effective and fast method to isolate viable and pure single cells, ensuring minimal manipulation of the cellular status. The core technology of the QIAscout is the QIAscout array, which is composed of 12,000 individual microrafts. Each microraft is 200 µm in length and 200 µm in width and is securely held within a micron-scale well of the QIAscout array. Within the QIAscout array, the microrafts serve as releasable culture sites for individual cells or colonies.

The QIAscout array is ideal for various cell types including adherent cells, suspension cells, cell lines, primary cells, and fluorescent cells providing an environment suitable for their growth and viability similar to any standard cell culture dish. QIAscout arrays are mounted on inverted microscopes and can be imaged by brightfield, fluorescence and confocal microscopy.

A motorized release device is mounted onto a 4x, 5x or 10x objective of common inverted lab microscopes to allow for selection and picking of individual microrafts. To isolate target cells, simply press the button on the controller which makes the release needle pierce through the lower surface of the QIAscout array and dislodge an individual microraft with your cell of interest attached. The released microraft is then recovered using a magnetic wand and transported to a secondary vessel (e.g., reaction tube of downstream application).
Steps in the QIAscout workflow include:
  • Seeding and cultivating cells in medium on the QIAscout array
  • Placing release device containing release needle on the microscope objective
  • Placing array on the microscope stage
  • Identifying microrafts containing single cells
  • Piercing microraft containing cell of interest
  • Transferring microraft to secondary vessel using a magnetic wand
  • Processing the collected cell for downstream application or further cultivation

The cell distribution on the QIAscout array follows a Poisson distribution (see Table “Cell distribution on the array follows a Poisson distribution”). To achieve the maximum number of microrafts on the QIAscout array containing a single cell and to minimize the number of microrafts with no cell or more than one cell, it is suggested to plate cells at a cell : microraft ratio of 1:2 or 1:3. A QIAscout array contains 12,000 individual microrafts, and therefore plating 4,000–6,000 cells is generally recommended. Adjust the cell density of your suspension and add the desired number of cells to the QIAscout array in 2 ml of medium.

Cell distribution on the array follows a Poisson distribution
Cell : Well ratio % Empty wells % Wells capturing a single cell % Wells capturing 2 or more cells
1:1 37 37 26
1:2 61 30 9
1:3 72 24 4
1:5 82 16 2
1:10 90 9 1

After adding cells to the QIAscout array, allow the cells to settle and wait until the cells have attached firmly enough to the microraft surface to allow for release and collection. A waiting time of 6–10 hours in culture is generally adequate, but the length of this period will be cell line-dependent. Once the cells are adhered to the microrafts, the QIAscout array can be screened under an inverted microscope to identify target cells and colonies and proceed with isolation and recovery.
The QIAscout is highly suitable for laboratories performing single-cell research. Single-cell isolation with QIAscout is compatible with multiple downstream applications such as:
  • Whole Genome Amplification
  • Whole Transcriptome Amplification
  • Single-cell Sequencing
  • Single-cell miRNA Analysis
  • Clonal Expansion

Have your throughput demands increased? Do you want to expand your application range or further streamline workflows? Do you need to manage more complex samples? Do you need improved connectivity?

If the answer to any of these questions is yes, then QIAGEN’s trade-in/trade-up program is just right for you!

QIAGEN makes it easy to keep up to speed with the latest automation and sample processing technologies. Simply exchange an old instrument for a new one. Improve your efficiency by trading in a competitor instrument or trading up with an older QIAGEN instrument.

Learn more about trade-in/trade-up opportunities.

Service Plans

Cat No./ID: 9245008
QIAscout, Basic Agreement, no PM
1 year coverage of shipping, labor, and spare parts. The instrument is repaired in a regional repair center with a turnaround time of 7-10 working days. The agreement does not include a preventive maintenance/inspection visit.
The QIAscout is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.


Altitude Up to 2000 m (6500 ft)
Applications Single-cell isolation
Connections Connect motor cable connector of the release device onto the controller until a snap-click sound is heard. To disconnect the motor cable, hold on to the connector and pull out the cable.
Consumables (supplied) QIAscout array with dimensions of 0.2 mm x 0.2 mm for each microraft.
Controls Controller; Input voltage: 12 VDC; Power: 6 W; Width: 94 mm (3.7 in); Depth: 132 mm (5.2 in.); Height: 46 mm (1.8 in.); Weight: 0.3 kg (0.66 lb)
Description Manual isolation of cells from a unique array on a petri-dish. Manual selection of microraft followed by piercing of microraft, collection of dislodged microraft and transfer to secondary vessel.
Dimensions Magnetic Wand; Size: Ø8 mm (0.3in.); Height: 55 mm (2.2in.); Magnetic Collection Plate; Width: 100 mm (5.9 in); Depth: 150 mm (3.9 in.); Height: 19 mm (0.7 in.); Release Device; Width: 44 mm (1.7 in.); Depth: 73 mm (2.9 in.); Height: 51 mm (2.0 in.); Release Needle Size; Diameter: 0.1 mm in the body; Diameter: 0.01 mm at the needle tip
Environmental class 3K2 (IEC 60721-3-3); 3M2 (IEC 60721-3-3)
Operating temperature 18–30ºC (64–86ºF)
Overvoltage category II
Place of operation For indoor use only
Pollution degree 2
Power supply AC Power Adapter; Width: 39 mm (1.5 in); Depth: 76 mm (3.0 in.); Height: 56 mm (2.2 in.); Weight: 140 g (0.31 lb); Input Voltage: 100–240 VAC; Mains supply voltage fluctuations are not to exceed ±10% of the nominal supply voltages; Input Current: 0.45–0.2 A; Frequency: 50–60 Hz
Relative humidity 10–80% (noncondensing)
Storage conditions Air temperature: 5°C to 40°C (41°F to 104°F) in manufacturer’s packaging; Relative humidity: Max. 85% (noncondensing); Environmental class: 1K2 (IEC 60721-3-1); 1M2 (IEC 60721-3-1)
Technical data of the instrument Device temperature: 30°C ± 10°C; Motor connection: Snap and lock connector; Insertion force: 4.5 kgs max.; Withdrawer force: 0.5–3.0 kg; Motor actuator speed: 400 steps/sec; Dislodging action: 1 needle with moving platform
Transportation conditions Air temperature: –25ºC to 60ºC (–13°F to 140°F) in manufacturer’s packaging; Relative humidity: Max. 75% (noncondensing); Environmental class: 2K2 (IEC 60721-3-2); 2M2 (IEC 60721-3-2)
Weight Magnetic Wand: 2.2 g (0.005 lb); Magnetic Collection Plate: 0.3 kg (0.66 lb); Release Device: 0.2 kg (0.44lb)

Product Resources

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