MiSeq System

The MiSeq System at the Department of Molecular Biology.

ImageMattias Pettersson

About MiSeq System

The MiSeq System from Illumina is an excellent low-throughput sequencer for applications such as bacterial whole genome sequencing or RNAseq. It utilizes Illumina’s SBS chemistry, the most widely adopted next-generation sequencing technology, which ensures exceptional data quality. This proprietary reversible terminator-based method enables the massively parallel sequencing of billions of DNA fragments, detecting single bases as they are incorporated into growing DNA strands. Fluorescent terminator dyes are imaged as each dNTP is added and then cleaved to allow incorporation of the next base. With all four reversible, terminator-bound dNTPs present during each cycle, natural competition minimizes incorporation bias. Base calls are made directly from signal intensity measurements during each cycle, greatly reducing raw error rates compared to other technologies. This results in highly accurate base-by-base sequencing, virtually eliminating sequence context-specific errors, even within repetitive sequence regions or homopolymers.

The MiSeq System features straightforward, easy-to-follow instrument control software, an intuitive touch screen interface, plug-and-play reagent cartridges with RFID tracking, on-screen video tutorials, and step-by-step guidance throughout each sequencing workflow.

The MiSeq System features an intuitive touch screen interface​.

ImageMattias Pettersson

The system includes onboard data analysis and access to BaseSpace™ Sequence Hub —Illumina’s genomic analysis platform— which provides real-time data uploading, simple data analysis tools, internet-based run monitoring, and a secure, scalable storage solution. BaseSpace also enables fast and easy data sharing.

Users produce their own libraries for sequencing, with various commercially available kits, including low input kits. Custom protocols can also be used. The MiSeq System processes a flow cell containing one lane, with run times of 8 hours (50 bp single read) to about 48 hours (300 bp paired-end read). The single lane flow cell can generate up to 25 million sequence reads per lane (V3 kit). Read lengths range from 50 bp single-end to 300 bp paired-end (600 bp).

For information about experimental design, library preparation kits and sequencing kits, contact Illumina (www.illumina.com).

Services and Offerings

The MiSeq System provides a comprehensive DNA-to-data sequencing platform, integrating cluster generation, amplification, sequencing, and data analysis in a single instrument.

Highlights

• Exceptional data quality: High-quality data demonstrated through peer-reviewed, scientific comparison.
• Simple, intuitive workflow: Highly automated system with an easy-to-use instrument interface.
• Fast turnaround time: Rapid sequencing and variant detection for time-critical studies.
• Extensive suite of applications: Adjustable read length and flow cell options provide ultimate flexibility across a broad range of applications.

Key applications

• Small genome sequencing
• Targeted gene sequencing
• 16S metagenomic sequencing
• Gene expression analysis with Targeted RNA-Seq
• Targeted gene panels
• De Novo Sequencing
• miRNA & Small RNA Analysis
• Genotyping by sequencing
• DNA-Protein interaction analysis with ChIP-Seq
• Quality Control

To learn more, visit illumina.com/systems/sequencing-platforms/miseq.

Note: we do not assist with experimental design, library preparation or analysis. Contact Illumina for such matters.

General policies and rules

GENERAL POLICIES AND RULES

1. Book the system through Artologik EZBooking (https://ez.artologik.net/umu-molbiol/fedauth/). Note: 1 day is the minimum booking period (morning to morning), and it is not permitted to book for more than 1 week at a time.
2. Before the first use, a mandatory training session is required. Contact responsible personnel.
3. It is recommended to reboot the system before a run (Windows > restart).
4. For sample sheet preparation in the LRM (Local Run Manager), use your LRM account. The responsible personnel will create the account the first time.
5. When setting up the run, user your own BaseSpace account to store/automatically upload the generated data. Base Space accounts can be created at Illumina (https://accounts.illumina.com/?ReturnUrl=https%3A%2F%2Fbasespace.illumina.com).
6. It is mandatory to sign up in the MiSeq logbook. Note: Fill in user, lab, date, starting time, ending time, method, and reagent-cartridge code.
7. After a run, the user is responsible for disposing of the residues following the University’s rules.
8. Important: perform a Post-run wash at the end of your run (check user guide). Do not remove the flow cell nor empty the wash tray or the wash bottle. This step is fundamental to prevent contaminations between experiments and to extend the system’s lifetime.
9. Never turn off the system.
10. MiSeq has limited storage capacity; therefore, all runs must be saved automatically in your BaseSpace account or elsewhere. Data stored on MiSeq will eventually be deleted.

Service fees

SERVICE FEES

Full day 650.00 SEK* (Minimum 24-hour booking period, morning to morning)

Discounts for frequent users within a 3-month period:

1. <10 booking days/3months: no discount
2. 10-20 booking days/3months: 15% discount
3. >20 booking days/3months: 30% discount

*Cancellation policy: The entire fee will be charged if the booking is not cancelled 24 hours ahead of use.

Availability

Available to research groups at Umeå University. External labs can potentially use the system upon availability (contact the RI director).

Location: Department of Molecular Biology, room 6K-11
Booking system: Artologik EZbooking

Mandatory training before first use.