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
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.
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 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 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