Services

Services

Getting Started

The staff have extensive knowledge and experience with the various platforms and can provide flexibility in project planning and implementation.

For questions about these services or to discuss your project, please email IHGSeqCore@ucsf.edu and our research specialists will respond promptly.

See our Pricing page

DNA Extraction

DNA Extraction

Our DNA Extrac­tion ser­vice pre­pares high qual­ity DNA sam­ples from blood (up to 10 ml) only. The DNA samples will be returned to you for storage, processing or shipment to collaborators.

Whole Exome Sequencing

Library Prep

Construction of libraries for Illumina sequencing

We can build a customized project for you based on our consultant rate and pass-through supplies. Please contact us at the email below.

Details
Genomic DNA sheared by Covaris S2 to a target size of 200-300bp and assembled into a library with TruSeq adapters containing indexes that differentiates different libraries in a capture reaction as well as a sequencing run.

Vendor: Kapa Biosystems


Exome Capture

To capture the coding regions of the genome

We can build a customized project for you based on our consultant rate and pass-through supplies. Please contact us at the email below.

Details
Libraries are pooled into a capture reaction that contains biotinylated DNA oligonucleotides (called ‘baits’), from Nimblegen, (SeqCap EZ Human Exome Library v3.0; Roche Nimblegen) for 72 hours. The DNA bait-DNA hybrids are then pulled out of the complex mixture by incubation with streptavidin-labeled magnetic beads and captured onto a strong magnet. After washing, the targeted DNA of interest is eluted and subjected to 18 cycles of DNA amplification.

Vendor: Nimblegen

Illumina Sequencing

Illumina HiSeq 2500

Next generation sequencing (NGS) for RNASeq, whole genome, whole exome and targeted DNA sequencing

Details
Choose high-output or rapid run

Run Mode High Output Rapid Run
Output Range 50-1000 Gb 10-300 Gb
Run Time <1-6 days 7-60 hours
Cluster Generation cBot  On Board
Reads per Flow Cell 2 Billion  300 Million
Maximum Read Length** 2 × 125 bp  2 × 250 bp
Type Turnaround TIme
High output PE 2x100bp flow cells ~7 days
Rapid PE 2x100bp flow cells ~28 hours
**High output PE 2x50bp flow cells ~4 days
**Rapid PE 2x50bp flow cells ~16 hours
High output SR 1x50bp flow cells ~3 days
Rapid SR 1x50bp flow cells ~8 hours

**Special ordering needed

Sequencing data will be made available to user via a Dell Workstation (with Dual Intel® Xeon® Processor X5560, 2.8GHz, 48G RAM) in gzipped fastq format (~50G bytes per PE lane) and transferred via a web portal.

Vendor Website:  Illumina

Affymetrix Axiom Genotyping

Affymetrix Axiom Genotyping and Expression

Genome-wide arrays (700k to 900k SNPs); Exome arrays (300k SNPs); Whole-transcript arrays

Details
We have 2 Beckman Coulter Biomek FXP Target Prep Express and 2 Affymetrix GeneTitan MC Instruments capable of running the Axiom World Arrays, Biobank Arrays, Exome Genotyping Arrays, Genome-Wide Population-Optimized Human Arrays, WT Arrays, and 3’ IVT Arrays.

Vendor: Affymetrix

Consultation

Consultation

Please email us at IHGSeqCore@ucsf.edu to set up a one-on-one free consultation to discuss your project.