IGI Next Generation Sequencing Core
IGI Next Generation Sequencing Core
Sequencing Services for IGI Investigators & Collaborators
Overview
The IGI Next Generation Sequencing Core (NGS Core) is a joint initiative of the Innovative Genomics Institute’s Center for Translational Genomics, the IGI Clinical Laboratory, and IGI Investigators.
The NGS Core was established to advance genome-engineering innovations by providing rapid, state-of-the-art, cost-effective, in-house sequencing services for IGI members.
We offer a growing range of services, from library construction to sequencing to complete experimental design and support. The sequencers that comprise the foundation of the NGS Core include two Illumina MiSeqs, an Illumina iSeq, and our highest capacity machine, an Illumina NextSeq2000. Together, these instruments provide IGI members with a flexible array of options and enable the NGS Core to support a broad range of applications and projects simultaneously.
Core Personnel
NGS Core Services
Research Sequencing
Whether you want to sequence a library that you generated yourself, or assistance creating the library, we can help. Our goal is to enable high throughput sequencing at economical recharge rates as an in-house service to your laboratory.
We understand that not all research is alike, so we’ve developed a range of NGS services to cover the spectrum of the IGI’s current NGS needs, as well as offer consulting services for custom experiments tailored to your research needs.
We are here to listen and create solutions.
1. CELL GENE EDITING NGS ASSAYS
To support your research, we currently offer the following:
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Partial Amplicon Library Prep and Sequencing: PCR2 + Bead Clean-Up + QC + Sequencing
Partial amplicon sequencing can be bespoke; you can share the run with other users (and share the cost) depending on your sequencing needs (sequencing depth and length), or you can run your samples on a single lane. |
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Full Amplicon Library Prep and Sequencing: PCR1 + PCR2 + Bead Clean-Up + QC + Sequencing
Sequencing can be bespoke; you can share the run with other users (and share the cost) depending on your sequencing needs (sequencing depth and length), or you can run your samples on a single lane. Please note: this service is currently only available to the IGI’s Clin1 projects. |
2. JUST SEQUENCING
If you just need a sequencing run on a single lane on one of the sequencers at the NGS Core:
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NEED MORE NGS RESEARCH OPTIONS?
We would be happy to meet with you to discuss any aspect of your project, including project design, custom library preparation, sequencing experiments, and data analysis.
Please contact netrak@berkeley.edu to schedule your consultation.
Pricing
Pricing is based on a cost-recovery model and will vary depending on the experiment and sequencing run requirements.
Each sequencer run can be customized or shared, depending on the user’s needs, such as read depth, read length, turnaround time, and the number of submissions for that week. Users will share the sequencing prices in 25% increments if sharing is an option.
Typical charges of the NGS Sequencing Core are detailed below. For an estimate, please email netrak@berkeley.edu.
CONSULTATION/CUSTOM DESIGN PREP
- IGI price: $67 per hour
- External price: $108 per hour
AMPLICON LIBRARY PREP COSTS
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Partial Amplicon Library Prep and Sequencing: PCR2+QC
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Full Amplicon Library Prep and Sequencing: PCR1+PCR2+QC (excluding custom primers)
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NGS RUN OPTIONS & COSTS
We use a variety of successful and widely adopted tools for conducting next-generation sequencing. Our technical infrastructure includes three Illumina sequencers: iSeq100, MiSeq, and NextSeq2000.
For recommendations about which type of sequencing run best suits your needs, please contact netrak@berkeley.edu to arrange a consultation.
iSeq — The iSeq is one of the low throughput Illumina sequencers offering up to 4 Million reads. The iSeq 100 offers the perfect solution for those wishing to run smaller projects on a dedicated run with fast turnaround times.
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KIT NAME |
READ LENGTH |
TOTAL READS |
TYPICAL RUN TIMES |
IGI PRICE PER RUN |
EXTERNAL PRICE PER RUN |
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iSeq 100 i1 Reagent v2/Micro v2 (300-Cycle) |
2 x 150 bp |
4 million |
20 hrs |
$712 |
$1143 |
MiSeq — The Illumina MiSeq enables diverse levels of output that range from 1 million to 25 million read-pairs. The instrument supports both single-end and paired-end cycles which require 1-3 days of run time. The MiSeq is ideal for small sequencing projects like small genome sequencing and target amplicon sequencing projects.
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KIT NAME |
READ LENGTH |
TOTAL READS |
TYPICAL RUN TIMES |
IGI PRICE PER UNIT |
EXTERNAL PRICE PER UNIT |
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MiSeq Kit v2 (300 cycles) |
2 x 150 bp |
15-20 Million |
30hrs |
$1430 |
$2296 |
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MiSeq Kit v3 (150 cycles) |
2 x 75 bp |
40 Million |
56 hrs |
$1263 |
$2027 |
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MiSeq Kit v3 (600 cycles) |
2 x 300 bp |
20-25 Million |
72hrs |
$2014 |
$3232 |
NextSeq 2000 — The Illumina NextSeq 2000 provides up to 1.1 Billion reads per run. Applications for NextSeq 2000 include single-cell RNA-seq, whole-exome sequencing, and small whole-genome sequencing. Sequencing on the NextSeq 2000 can take up to 2 days.
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KIT NAME |
READ LENGTH |
TOTAL READS |
TYPICAL RUN TIMES |
IGI PRICE PER RUN |
EXTERNAL PRICE PER RUN |
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NextSeq 1000/2000 P1 Reagents (300 Cycles) |
2 x 150 bp |
100 million |
24 hours |
$1672 |
$2684 |
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NextSeq 1000/2000 P2 Reagents (300 Cycles) v3 |
2 x 150 bp |
400 million |
30 hours |
$4208 |
$6754 |
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NextSeq 2000 P3 Reagents (300 Cycles) |
2 x 150 bp |
1.1 Billion |
40 hours |
$6832 |
$10,966 |
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A Note About Turnaround Time Sequencing time depends on the type of run and number of cycles, with typical run times shown in the tables above. Once samples arrive at the NGS Core, the total turnaround time includes library prep, time in the sequencing queue, and sequencing run time. The size of the sequencing queue is highly variable; thus, the wait time for sequencing your sample is often difficult to predict. Upon sample submission AND arrival, your samples are entered into a queue and run on the next available FULL run that matches your run type. We do our best to give you the fastest turnaround time to support your research project. |
FULL SERVICE LIBRARY PREP & INVESTIGATION DESIGN
Our Full-Service options and custom Investigation Design are prepared and sequenced at a per-sample plus consultation hourly rate. Please contact netrak@berkeley.edu to discuss your experiment design and obtain a price quote.
Sample Preparation
To ensure successful sequencing, all samples submitted to the NGS Core must adhere to our current guidelines. Find the sample preparation guidelines here.
Ordering
Please contact netrak@berkeley.edu to request an initial consultation. Please include the following information in your email: 1. Your name; 2. Lab/PI name; 3. PI email.
After your consultation, please allow up to 3 business days for your profile to be set up. Once you are registered, you will receive two automatic emails:
- The first email (Lockbox Login Information) gives you details of your username and a link to set your password. Please set up your login credentials with the username provided. Do not use the “SSO” link for now. After setting your password, you may need to set up two-factor authentication. Please follow the instructions on the screen for this.
- The second email (Welcome to CTG NGS Submission Portal) confirms that you have set up your profile and shares the Submission portal homepage link.
To ensure successful sequencing, all samples submitted must adhere to the following guidelines.
Please log in to the NGS Core portal and enter your username and password.
Please watch our portal video for detailed instructions on submitting your project and seeing project status updates.
You can also find step-by-step portal instructions here: NGS Core Portal Instructions.
There are specific requirements for the storage and transport of your plates. This document describes these requirements and offers recommendations for courier and shipping to ensure your plates arrive safely.
Please log in to the NGS Core portal. Once logged in, the Home Page contains information about your projects and their status for you to track the progress of your submission.
If you are a PI, not only can you view projects that you have submitted, but you can also view and track all of your team’s projects.
When sequencing is complete, you will receive an email with all the details, including information about downloading data. You will need an Illumina BaseSpace account. This account is free and allows you to save and download the data indefinitely. Please create an account if this is your first time using Illumina BaseSpace.
Billing and Invoicing
The NGS Core uses the UC Berkeley Recharge system. The NGS Core Recharge unit is only available to IGI members and allows you to use your chartstrings to pay for our services easily.
Quotes for our standard services are generated automatically for orders through our online NGS Core submission portal.
During order submission, you must enter a valid chartstring from the list, which the user has been authorized to use. If your chartstring is not on the list, please email netrak@berkeley.edu (copy your PI on this email) with the following information:
- Unit
- Fund code
- Org/Dept
- Program
- Chartfield 1
- Chartfield 2
- Funding source end date
- Members authorized to use the funds
Please note that when team members use any funding source/chartstring for their projects/submissions, they need to accept the responsibility that they are authorized to use that chartstring by checking a box. Once checked, we assume they are authorized to use this funding source. It is the responsibility of the PI, lab manager, or finance personnel to keep track of the charges.
The IGI will transfer funds from your account at the end of each month. Pre-billing is not allowed for federally funded work. If your funds are expiring and need urgent billing, please let us know before submitting your work.
Contact Us
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Consulting, experimental design, quotes, contracts, and other inquiries |
Netravathi Krishnappa, M.Sc. |
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Director of IGI NGS Core |
Petros Giannikopolous, MD |