Sample Processing

Sample Processing


Affymetrix Axiom Genotyping and Expression

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 Website: Affymetrix
Price: See Pricing page

CONTACT

IHGSeqCore@ucsf.edu


Illumina HiSeq 2500

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
Price: See Pricing page
Additional costs apply. Depending on the complexity of the sequencing project and QC of sequencing samples, we charge 1-3 hours as genomics consultation. The GCF recommends that users purchase their own reagents and ship them to HSW901A, 513 Parnassus Ave., San Francisco, CA 94143 (Attn: Richard Lao). We can help arrange the sharing of flow cells.

CONTACT

IHGSeqCore@ucsf.edu

Consultation

Consultation

Price: See Pricing page

CONTACT

Contact the person listed in the service you require

 

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

To discuss your project, please send an email to IHGSeqCore@ucsf.edu and our research specialists will respond promptly.

Service contacts are

Richard Lao richard.lao@ucsf.edu 415.514.3879
Eunice Wan eunice.wan@ucsf.edu 415.514.3879