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Compact CE Sequencer DS3000

Compact CE Sequencer DS3000

A compact, convenient, easy-to-use DNA sequencer

The DS3000 inherits the same core capillary electrophoresis technology developed by Hitachi High-Tech over many decades – now in a compact, easier than ever to use, system.
Sequencing analysis and fragment analysis can be performed easily.

Sales area: Japan, China, Korea, Taiwan, Hong Kong


Intuitive and easy-to-use touch screen panel

The screen is equipped with a touch-panel GUI that saves space and improves operability. System management and run conditions can be reviewed at a glance simplifying the genetic analyses process.


The intuitively designed touch screen panel puts ease of use and operability first.
The four main operations of Run Measurement, Review Results, Maintenance, and Protocols are clearly displayed.
The detail of each operation is available at a single touch.

Easy to install cartridge system

The DS3000 adopts easily installable cartridges for the capillaries and reagents.


Reduced maintenance frequency

  • No need to clean a pump
    By developing a syringe-type polymer cartridge having a high-durability movable seal, and making the liquid transport system pump-less, eliminates pump maintenance.
  • No need to remove bubbles
    By adopting an unique polymer injection system, it is not necessary to remove bubbles at the time of polymer filling, reducing excess polymer consumption.
  • Less frequent light source replacement
    Pulse signal control means LD is only on during detection. The shortened illumination time increases the useful lifespan, especially when compared to complicated and expensive light sources such as Argon gas lasers.

Reduced footprint

The incorporated touch screen has reduced the DS3000 to the compact dimensions of 400 mm wide × 600 mm deep × 600 mm high.


Enhanced user convenience

  • Equipped with remote monitoring system
    By incorporating a remote monitoring system, it is possible to monitor the instrument state, set assay conditions, display analysis results, and prepare reports from a Web browser.
  • Utilizes an ordinary general-purpose PC to reducing set-up costs
    The instrument can simply be added to existing networks with secondary analysis and reporting allocated to a standard PC.

Application [Sequencing analysis]

Contiguous Read Length


Sequencing was performed using the BigDye® Terminator v3.1 Sequencing Standard Kit in Standard Sequencing mode. The electropherogram data display demonstrates high resolution and accurate QV values were maintained at 500 bp. Contiguous Read Length of 600 bp or higher in Fast Sequencing mode, or at 700 bp or higher in Standard Sequencing are typical and reproducible.

Application [Fragment analysis]

Human Identification (HID)


200 pg of 2800 M control DNA was amplified with a PowerPlexTM Fusion 6C System, and subjected with the Promega® 6 dye system compliant electrophoresis module. The obtained (fsa), file was analyzed and visualized by a secnodary software, GeneMarker HID.

*  The electropherogram view is obtained from GeneMarker HID (SoftGenetics, LLC, sold separately)

Technical Report

The details can be found on the membership site "S.I.navi" (registration is free).

No. Overview Issue date
HTB-DS-E016 Examples of microbial identification using the DS3000 Compact CE Sequencer
When using the DS3000 Compact CE Sequencer, the operator can choose the optimal polymer for the analysis from Polymer4 or Polymer7. Polymer7 is mainly used for sequencing analysis, but can also be used for fragment analysis. Here, we describe the performance of Polymer7 for fragment analysis using the GenePrintTM 24 System (Promega🄬).
HTB-DS-E015 Improvement of reading accuracy of short DNA using the DS3000 Compact CE Sequencer
In Sanger sequencing, the quality of the peak shapes may not be good enough to identify the correct base in the beginning of the electropherogram. This is because the sieving matrix for electrophoresis (polymer) filled in the capillary may not be able to detect and separate short DNA properly. This report introduces an example of improving the data quality in the beginning of the electropherogram using a sequencing primer equipped with a tail on the DS3000 Compact CE Sequencer.
HTB-DS-E014 Example of GC-rich sequence analysis using the DS3000 Compact CE Sequencer
Sequences rich in guanine (G) and cytosine (C) (GC-rich sequences) are often found in functionally important positions on the genome such as transcription control regions. GC-rich sequences inhibit polymerase extension reactions, resulting in failure to obtain expected products in the polymerase chain reaction (PCR) and the cycle sequencing reaction.
HTB-DS-E013 Example of MLPA🄬 analysis using a DS3000 Compact CE Sequencer
The MLPA🄬 method (Reagent Manufacturer: MRC Holland, Reagent Distributor inJapan: FALCO biosystems Ltd.) is widely used to analyze copy number variation (deletions/duplications: CNV), known SNP, and methylation status. Sequences that specifically hybridize to the target gene are designed within the MLPA🄬 probe, and mutations are analyzed by capillary electrophoresis through hybridization, ligation, and PCR. An example of MLPA🄬 analysis using the DS3000 Compact CE Sequencer (DS3000) is presented here.
HTB-DS-E012 SNaPshotTM analysis using the new functions of the DS3000 Compact CE Sequencer
A new function has been added to the DS3000 Compact CE Sequencer (DS3000). With the new DS3000, you can now customize the fluorescent dyes and size standards used in your analysis. You can also use more reagent kits. As an example of the enhanced utility of the DS3000 with the added function, SNaPshotTM (Thermo Fisher Scientific) was performed using a combination of fluorophores that was not supported by the previous DS3000.
HTB-DS-E010 NGS data confirmation using the DS3000 Compact CE Sequencer
Due to the ease of the analysis, genomic variations detected by next-generation sequencing (NGS variants) are sometimes confirmed by Sanger sequencing (1). Here, we introduce a practical example of confirming NGS variants using the DS3000 Compact CE Sequencer (DS3000).
HTB-DS-E009 Analysis of rare variants with the DS3000 Compact CE Sequencer and Mutation Surveyor
Rare variants are mutations that are found in a small subpopulation of specimens. They have been recognized for their usefulness in cancer research, because they can cause tumorigenesis and promote tumor progression. The signals from rare variants are buried behind the signals from wild-type DNA, which comprises the vast majority of DNA in samples. Therefore, the detection of rare variants requires very high sensitivity and accuracy.
HTB-DS-E008 Bisulfite Sequencing with the DS3000 Compact CE Sequencer
Of the four bases that make up genomic DNA in higher eukaryotes, the fifth carbon of cytosine can be methylated by a methyltransferase. Cytosine methylation plays an important role in various events that occur on genomic DNA, including the regulation of gene expression, and it is known as a representative epigenetic marker.
HTB-DS-E007 Cell Line Authentication with the DS3000 Compact CE Sequencer
Cell line contamination, misidentification, and genetic drift result in invalid research. It has been estimated that 18% to 36% of cell lines are contaminated or misidentified (1). To address this issue, a number of scientific journals request researchers to perform cell line authentication (CLA) prior to submitting a manuscript that involves the use of cell lines (2).
HTB-DS-E006 Effect of sample injection conditions on performance of DS3000 Compact CE Sequen
With the DS3000 Compact CE Sequencer (hereinafter, the “DS3000”), DNA molecules are injected into a capillary array as a result of the difference in electrical potential between the anode and the negatively charged DNA molecules. The magnitude and duration of the applied voltage (hereinafter , the “injection voltage” and “injection time”, respectively) have a significant effect on the number of molecules injected and the peak resolution,thereby affecting the accuracy of electrophoresis measurements.
HTB-DS-E005 Fragment analysis using Polymer7 with DS3000 Compact CE Sequencer
When using the DS3000 Compact CE Sequencer, the operator can choose the optimal polymer for the analysis from Polymer4 or Polymer7. Polymer7 is mainly used for sequencing analysis, but can also be used for fragment analysis. Here, we describe the performance of Polymer7 for fragment analysis using the GenePrintTM 24 System (Promega🄬).
HTB-DS-E004 Detection of Shellfish Allergens using DS3000 Compact CE Sequencer
Food allergies occur in approximately 1-3% of adults and 4-6% of children [1] and occasionally can cause life-threatening symptoms. Thus, detection of food allergens and labeling of them on food products are critical issue for food safety. Although protein allergen can be detected directly by a conventional method such as ELISA, nucleic acid-based assay, which enables detect DNA sequences coding allergens, is sometimes employed because of its higher sensitivity, less cost and better ease-of-use.
HTB-DS-E003 Microsatellite Instability Analysis using DS3000 Compact CE Sequencer
Microsatellite instability (MSI), an accumulation of somatic mutations in microsatellites or short tandem repeat sequences, is a consequence of DNA mismatch repair (MMR) system deficiency, and thus considered as a biomarker for multiple types of cancers. In MSI analysis, DNA fragments were distributed in single-base resolution and compared with the reference data on a capillary electrophoresis (CE).


■Main unit specifications

Item Details
Number of capillaries 4
Capillary length 36 cm
Sample format 8-tube strip × 4
Device control Touch panel PC
Number of Dyes 6
Application Sequencing analysis / Fragment analysis
Size 400 (W) × 600 (D) × 600 (H) mm
Weight 45 kg
Performance guarantee temperature 15 – 30°C
Performance guarantee humidity 20 – 80% RH (no condensation)
Power input 100 – 240 ±10% VAC,50/60 Hz
Rated power 260 VA
Supported secondary analysis software
  • Mutation Surveyor (SoftGenetics, LLC, sold separately)
  • GeneMarker (SoftGenetics, LLC, sold separately)
  • GeneMarker HID (SoftGenetics, LLC, sold separately)

■Run module specifications

Run Module Application Polymer
Contiguous Read Length*1
(bp, QV20 CRL)
Average run time
Fast_Sequence36_Polymer7 Sequencing analysis Polymer7 ≥600 ≤32
Standard_Sequence36_Polymer7 Sequencing analysis Polymer7 ≥700 ≤60
BDx_Fast_Sequence36_Polymer7 BDx sequencing analysis Polymer7 ≥600 ≤32
BDx_Standard_Sequence36_Polymer7 BDx sequencing analysis Polymer7 ≥700 ≤60
Run Module Application Polymer
Average run time
Sizing precision*2
Fragment_Analysis36_Polymer7 Fragment analysis Polymer7 ≤35 NA
Fragment_Analysis36_Polymer4 Fragment analysis Polymer4 ≤44 <0.16

■Consumables specifications

Product name Part number Details Remarks
Capillary Cartridge 36 cm 613-0330 1 pcs Storage temperature:
15 – 30°C
Buffer 613-0252 Anode Buffer × 2 cartridges
Cathode Buffer × 2 cartridges
Storage temperature:
2 – 10°C
Polymer7 613-0251 4 cartridges Storage temperature:
2 – 10°C
Polymer4 613-0250 4 cartridges Storage temperature:
2 – 10°C
Septa for Cathode Buffer Cartridge 613-7231 10 pcs  
Retainer for Cathode Buffer Cartridge 613-7233 4 pcs  
Septa for 8 well tubes 613-7230 24 pcs  
Base and Retainer for 8 well tubes 613-7232 4 pcs  
Anode Electrode Assembly 613-7263 1 pcs  

*1 Contiguous Read Length (bp, QV20 CRL) is measured with BigDye® Terminator v3.1. Sequencing Standard Kit (Thermo Fisher Scientific, sold separately)

*2 Sizing precision (bp,50~400bp) is measured with PowerPlexTM ESI17 Fast Allelic Ladder and WEN ILS 500 ESS. (Promega, sold separately)

* BigDye is a registered trademark of Thermo Fisher Scientific Inc.

* Promega, PowerPlex is a registered trademark of Promega Corporation.

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