NGI OpenLab
NGI OpenLab is a user-accessible lab space at SciLifeLab Uppsala (BMC), where researchers can run sequencing workflows independently or with guidance, from QC and library prep to sequencing on a walk-up sequencer.
NGI OpenLab is a new interactive lab space designed for collaborative work with NGI’s users. The lab provides direct access to equipment for quality control (QC), library preparation and a walk-up sequencer for on-the-go sequencing needs.
Our mission is to create a hands-on, interactive environment where researchers can expand their skills in genomics through practical experience, training sessions and courses. The OpenLab space is equipped with basic genomics instrumentation and has NGI genomics experts available. This service allows users to perform quality control, prepare samples for genomics assays and test new methods independently or with guidance. NGI OpenLab is being launched as a pilot initiative available at NGI in Uppsala, SciLifeLab (Biomedical Center, BMC).
Explore the options below to learn how you can access NGI OpenLab, and feel free to reach out with any questions!
For inquiries about NGI OpenLab, please contact our project coordinators at NGI via support@ngisweden.se
Equipment List and Lab Space Overview
The NGI OpenLab is a user-interactive hub featuring tools for quality control (QC), library preparation and a benchtop sequencer for on-the-go sequencing needs.
Below is a list of available equipment and reagents in the NGI OpenLab:
The laboratory space features an entrance area equipped with lab coats to ensure safety and cleanliness in the lab, and a storage space for personal belongings. The lab space is organized into distinct workstations, tailored to specific applications, such as sample quality control, library preparation, and sequencing.
Fees
The cost for using NGI OpenLab includes a User Licence and Lab Introduction fee. This fee covers a mandatory introductory course. After completing the introductory course, you will be issued with a user license that allows you to use OpenLab. Other costs include fees for reagent usage and staff support. The fees below apply to users within Swedish academia. For users outside of Swedish academia, please contact us for a quote.
Below is a detailed breakdown of costs for various services and work areas available in OpenLab:
How to get started with NGI OpenLab
Follow these steps to set up your access and get started with NGI OpenLab!
Please refer to the FAQ section below for additional information. For any additional questions, feel free to contact us at support@ngisweden.se.
1. Book the Introductory Course
The first step is to contact support@ngisweden.se to book an on-site introductory course at the NGI OpenLab space. This mandatory, fee-based course will be held together with our staff members who will walk you through the practicalities of the lab space.
Training on QC instruments and a basic introduction to specific workstations in the lab can be included in the introductory course, depending on your needs in the lab space. Upon successful completion of the course you will receive your user license.
All users of NGI OpenLab must have a valid user license to use the lab space.
If sequencing is required, a separate sequencing introduction course is required after the general introductory course. Please refer to the Fees section above for cost details of the specific introductory/training courses. The general course and the sequencing course can be held at the same time. More information about sequencing in the OpenLab can be found further down in the section Sequencing in NGI OpenLab.
2. Provide Contact Information and an Invoice Address
To complete the registration process, you (PI and user) must provide your contact details (email and phone number) and an invoice address. This information is required for invoicing purposes, invoices will be sent on a regular basis after each usage of the lab’s resources.
This information will be requested during communication with the NGI OpenLab Staff members when booking the introductory course.
3. Sign the User Agreement
Before attending the introductory course, you will need to sign a user agreement. This agreement outlines the terms and conditions of lab use, ensuring that you understand and adhere to the NGI OpenLab policies. The agreement must be signed by both the intended NGI OpenLab User and the PI and financially responsible person.
The agreement will be sent to you during communication with the NGI OpenLab Staff members when booking the introductory course.
4. Access the Booking Calendar
Once you have signed the agreement and obtained your user license, you will gain access to the NGI OpenLab booking calendar. This allows you to independently reserve lab time for your specific needs.
Remember to remove/cancel your booking from the booking calendar if something unforeseen happens and you are unable to use your booked slot. It is very important to free up the slot for other users of NGI OpenLab if you are unable to use it.
5. Collect/Return Your Access Card
During your introductory course, you will be provided with instructions on how to collect and return your access card.
- Collect your card: When you have completed the steps above and booked a time in the calendar, you will be given an access card that allows you to enter the NGI OpenLab facility. Instructions on how and where to collect your access card will be given during the introductory course.
- Return your card: When you're finished with your work in the lab, the card must be returned in the designated mailbox located in the lab, along with your cost specification that will be used for invoicing.
The access card is for temporary use only and must be returned immediately after each session or use of the lab space. It is not for extended loan, as it is shared with other NGI OpenLab users who also require access to the lab.
6. Log Your Usage of Lab Resources in a spreadsheet
Users are required to log the usage of reagents and materials in a designated cost spreadsheet that is available in the lab. Once you have completed your work in the lab, fill in the spreadsheet and place it, along with your access card, in the designated mailbox in the lab.
The information in the spreadsheet will be used to generate an invoice, which will be sent regularly to the invoice address provided during registration.
7. NGI OpenLab Staff
The concept behind NGI OpenLab is to enable users to work independently in the pre-booked lab space, therefore NGI OpenLab staff members will not be regularly present in the NGI OpenLab. However, NGI OpenLab staff members will be available on call and can be contacted for assistance with urgent questions or issues that require immediate support.
Staff availability is guaranteed for phone support between 9:00 AM and 3:00 PM, Monday to Friday.
Support might not be available on national holidays and bridge days. Days with no support available are tagged in the booking calendar.
During your introductory course, staff members will be present to guide you on the practicalities for independent work in the lab. Additionally, the NGI OpenLab staff are available for hands-on support for specific project requests, which must be pre-booked in advance.
Sequencing in NGI OpenLab
The sequencer available in NGI OpenLab is an Illumina MiSeq i100 Plus.
For detailed information regarding output, runtime, and available flow cells, please visit Illumina’s official website: https://emea.illumina.com/systems/sequencing-platforms/miseq-i100.html
How to get started with sequencing in NGI OpenLab?
To gain access to the sequencer, you must first complete the General Laboratory Introduction Course either before or in connection with the NGI OpenLab MiSeq i100 Sequencing Course.
What do I need to prepare before the sequencing course?
Sequencing library and kit:
For the sequencing introductory course, you’ll need to bring your prepared sequencing library (2-10 nM) and the sequencing kit you intend to use. Kits can be ordered from Illumina’s website under MiSeq i100 Series Reagent Kits
PhiX, and a USB stick for data retrieval are provided by NGI Open Lab. Before the course begins, it is important that you consider and decide:
- How much of your library to load onto the instrument to ensure optimal data output.
- How much PhiX to add to your library.
Helpful guidelines can be found here: Loading Concentration Optimization Recommendations for the MiSeq i100 Series | Illumina Knowledge and in the NGI OpenLab MiSeq i100 Plus Instructions (see below).
QC and pooling of libraries:
Prior to the sequencing course, library QC and pooling can either be performed at NGI OpenLab (requires a User License) or in your own lab. QC reagents for the sequencing library are available if needed.
Required Reading:
You need to prepare by reading the NGI OpenLab MiSeq i100 Plus Instruction document before the sequencing course. It is also important to review the relevant sections of Illumina’s documentation referenced in that document.
Sample sheet preparation:
You need to prepare a sample sheet for sequencing using Illumina BaseSpace Sequencing Hub. A guide for creating the sample sheet in BaseSpace is available below. Using this tool, the sample sheet can be directly downloaded to the NGI OpenLab MiSeq i100 Plus instrument.
Index guidelines for Illumina sequencing can be found on our homepage: NGI Sweden » Index guidelines for Illumina sequencing
Policy Guidelines and Acknowledgement
As a user of NGI OpenLab, it is important to follow the lab's rules and safety guidelines. NGI OpenLab operates on trust, mutual respect, and a shared commitment for taking care of the equipment and the common lab space.
Download the PDF file below to review our User Agreement for using NGI OpenLab including Policy and Safety Guidelines:
Acknowledgement
The use of NGI OpenLab resources must be properly acknowledged in any presentations or publications resulting from your work in the lab. In addition to the acknowledgment text provided in the report accompanying your data, please include the following sentence:
"This project was supported by NGI OpenLab."
Apply for an NGI OpenLab User License
If you are ready to get started with NGI OpenLab, email your request to support@ngisweden.se and we will help you with the process! The NGI OpenLab space is located at NGI in SciLifeLab Uppsala (Biomedical Center, BMC).
Please refer to the FAQ section below for additional information.
Frequently Asked Questions (FAQ)
Lab Access, Courses, and Payment
How do I book the lab?
Once you have completed the introductory course and received your user license, you will be granted access to the NGI OpenLab booking calendar. You can then independently reserve lab time based on your needs.
Please remember to remove/cancel your booking from the booking calendar if something unforeseen happens and you are unable to use your booked slot. This will free up the slot for other users of NGI OpenLab.
When can I access the lab?
The lab is available for booking during regular working hours, Monday to Friday. You can access the lab using your access card, which you can collect after booking the lab. Instructions on how and where to collect your access card will be given during the introductory course.
Please note, staff availability is guaranteed for phone support between 9:00 AM and 3:00 PM, Monday to Friday.
Will the courses in OpenLab give me formal university credits? No, unfortunately not.
How do I collect and return my access card?
- Collect your card: During your introductory course, you will be provided with instructions on how to collect and return your access card.
- Return your card: When you're finished with your work in the lab, the card must be returned in the designated mailbox located in the lab, along with your cost specification that will be used for invoicing.
Can I bring a friend?
No. Anyone entering or using the lab must attend the introductory course to receive a user license before they are allowed in the lab space.
How do I pay?
In the lab, there are cost spreadsheets available where you must log the reagents and materials used. Once you have completed your work, fill in the spreadsheet and place it, along with your access card, in the designated mailbox in the lab. The information in the spreadsheet will be used to generate an invoice, which will be sent regularly to the invoice address provided during registration.
Reagents & Sequencing Kits
What reagents and consumables are available in the lab?
A detailed list of equipment and reagents available in the lab are found in the section above: Equipment List and Lab Space Overview. This includes, for instance, reagents/consumables for TapeStation, Qubit, etc., and is available at a cost per sample (see cost details in the section above: Fees).
Can I buy a sequencing reagent kit from you?
No, not at the moment. To avoid charging for potential reagent waste/unused left-over reagents, we currently require our users to order their own kits. However, if we notice a high demand for a specific type of flow cell and read length, this policy may change in the future.
Consumables and Phix for the sequencing run is available in NGI OpenLab, as well as a USB stick to transfer the data. These are included in sequencing starting fee.
Can I bring my own reagents?
You are welcome to bring your own reagents, such as specific library prep kits or preferred QC-kits that are not available for direct purchase in the lab.
Can I store my reagents and samples in the lab over night?
Yes. The freezers and fridge can be used for short term storage. Please make sure to label the reagents and samples with your name. Note! The fridge/freezer is not connected to a freezer alarm and NGI does not take responsibility for the reagents stored inside.
Sequencing & Data Management
I’ve lost my sequencing data/the sequencing data download is corrupt – do you have a back-up?
No, after the sequencing run it is your responsibility to make sure that you have copied the files needed to the UBS stick that we provide in NGI OpenLab. After the copy is complete, we ask you to delete the run from the instrument.
I made a mistake in my samplesheet and the samples were not properly demuliplexed, what do I do?
We recommend you to use the following script for demultiplexing: GitHub - Molmed/fastq_demux: Demultiplex Illumina FASTQ files
Lab Support & Troubleshooting
Who do I call for help?
NGI OpenLab staff members will be available on call and can be contacted for assistance with urgent questions or issues requiring immediate support. Contact details will be displayed in the NGI OpenLab space if you need to reach staff members.
My instrument shut down/there is no reagent available – what do I do?
NGI OpenLab staff members will be available on call and can be contacted for assistance with urgent questions or issues requiring immediate support. Contact details will be displayed in the NGI OpenLab space if you need to reach staff members.
Will there be staff members in the lab?
The NGI OpenLab is designed for independent use, meaning staff members will not be regularly present in the NGI OpenLab. However, NGI OpenLab staff members will be available on call and can be contacted for assistance with urgent questions or issues requiring immediate support (see FAQ Who do I Call for help).
Additionally, the NGI OpenLab staff are available for hands-on, fee-based support for specific project requests, which must be pre-booked in advance.