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.

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:

Partial Amplicon Library Prep and Sequencing: PCR2 + Bead Clean-Up + QC + Sequencing  You design the primers for PCR1 (along with the stubs, see this document for details) and submit cleaned, quantified (nanodrop/qubit/picogreen) libraries post-PCR1+BeadClean.  We accept post PCR1 and purified libraries. Then, we prepare the rest of the Library prep, including Indexing PCR, BeadClean, and QC (Qubit, Fragment Analyzer, and qPCR), and sequence.  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.

Full Amplicon Library Prep and Sequencing: PCR1 + PCR2 + Bead Clean-Up + QC + Sequencing You submit quantified DNA samples. We can assist in designing your primers which you ship along with your samples. We prepare the full amplicon library prep (PCR1+PCR2+BeadClean), QC (Qubit, Trace analysis, and qPCR), and 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:

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

	Partial Amplicon Library Prep and Sequencing: PCR2+QC IGI price: $14 per sample External price: $22 per sample
	Full Amplicon Library Prep and Sequencing: PCR1+PCR2+QC (excluding custom primers) IGI price: $18 per sample External price: $30 per sample

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.

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.

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.

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

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