Stanford Functional
Genomics Facility

High Throughput Sequencing

High-throughput sequencing services are available from The Stanford Functional Genomics Facility for investigators associated with Stanford University, Stanford Cancer Center, and affiliates. The facility currently supports DNA/RNA sequencing using the Illumina Genome Analyzer IIx (commonly referred to as "Solexa") for reads up to 76 bases for both single and paired-end runs. The Solexa technology supports methylation studies, SNP genotyping, ChIP-Sequencing and gene expression analysis. Pricing is dependent on run base length and choice of single end or paired end method of sequencing


Illumina GAIIThe Illumina sequencing technology utilizes hybridization and amplification on a multi-lane glass flow cell to produce hundreds of thousands of DNA clusters per lane. After amplification, each cluster is sequenced directly by use of reversible terminator dye chemistry. Up to eight samples can be sequenced at a time on the Solexa system. Library creation is generally done by the customer and supplied “ready to run” to the SFGF core lab. We suggest checking the quality of the library using qPCR or the Agilent BioAnalzer system. Additional information on optimizing library creation can be found here.

Quality Control

Every run includes a commercially available reference sequence (PhiX 174 DNA) to determine run quality. Sequence data from each run is filtered for sequence and alignment quality. Final sequence assembly after base calling, alignment and quality control checks are included in all sequencing runs.

To get a project started, fill out our online request form. For inquiries not addressed by this site or the FAQ, please send your request to

Footer Links: