Functional Genomics Facility


Overview of Services


The Stanford Functional Genomics Facility (SFGF) provides assays, services, and equipment for cutting edge genetic and genomic based research. 


SFGF is currently accessible and available to assist the Stanford research community with any COVID-19 related research projects.  Please indicate in your iLabs request that the service being requested is COVID-19 related or in support of critical and essential research.  Please contact Luisa Jimenez ( or John Coller ( if any assistance is needed.   



Available Services: 

  • High-throughput Sequencing and Library Construction utilizing Illumina MiSeq, NextSeq, HiSeq 2000, and HiSeq 4000
  • Single-Cell RNA-Seq utilizing 10x Genomics Chromium
  • Single-Cell RNA-Seq from FACS sorted cells 
  • Gene Expresion Assays - Microarray Platforms: Affymetrix, Illumina, Agilent
  • Whole Genome Genotyping Assays - Microarray Platforms: Illumina and Affymetrix
  • Karyotyping (Illumina)
  • Gene Expression and Genotyping using real-time PCR 
  • Digital PCR (BioRad)
  • Nanostring single molecule counting
  • Bioanalyzer DNA, RNA and Protein analysis, Qubit quantification, DNA shearing on Covaris
  • Sample Tracking, Sample Contamination and Cell Line Authentication Services
  • TALEN construction
  • Custom Array Printing of any material
  • Preferred pricing on Custom Oligonucleotides from IDT - Stanford-IDT Portal
  • Streamlined ordering and preferred pricing for Oligo Pools from Agilent


Available Equipment 24/7:  (You can request 24/7 access to the following equipment by going to the Request Services tab and selecting SFGF 24/7 Access)

  • Sequencers:  Illumina iSeq 100, MiSeq, NextSeq
  • Real-time PCR:  QuantSutio 12K Flex, ABI 7900HT, ABI StepOnePlus, Roche LightCycler 480, Stratagene MX 3005p
  • Microarray Scanners:  Agilent Scanner, Axon Scanner
  • Imagers:  GE Typhoon TRIO, LiCOR Odyssey, Alpha Imager
  • Quanitation:  Bioanalyzer, Nanodrop, Qubit 2.0 and 3.0 Fluorometers
  • Automation:  Biomek FX, Agilent Bravo, Formulatrix Mantis, Microarray Printer, NuGEN Mondrian
  • General Equipment:  Tetrad PCR Machines 


Getting Started

  • Stanford Users:  LOGIN or REGISTER for an iLab account using valid Stanford credentials (SUNet ID).




John Coller, PhD | SFGF Director

Office: CCSR 0120  -  (650) 736-1026

Lab: CCSR 0120  -  (650) 736-2434

Email:  john.coller at



Name Role Phone Email  Location

Luisa Jimenez

Administration 736-1763 luisaj at CCSR 4256

Alain Boussard

Programmer 736-1763 alainb at CCSR 4256
Xuhuai Ji

High Throughput Sequencing (MiSeq)

NGS Library Preparation

NGS Sample QC

736-2434 xuhuai.ji at CCSR 0120
Vanita Natu

Genome Wide Genotyping

NGS Library Preparation

Sample Tracking and Cell Line Authenication

NGS Sample QC

736-2434 vanita at   CCSR 0120
Vida Shokoohi

Genome Wide Gene Expression

PCR Gene Expression and Genotyping

NGS Library Preparation

DNA and RNA Sample Extraction and QC

736-2434 faraz at CCSR 0120
Dhananjay Wagh

High Throughput Sequencing (NextSeq)

Digitial PCR

Biomolecule Binding Assays

NGS Sample QC

736-2434  dwagh at CCSR 0120


Location and Hours of Operation





Stanford Functional Genomics Facility 
CCSR 0120
269 Campus Drive 
Stanford, CA 94305-5177 


Mailing Address:

Stanford Functional Genomics Facility
CCSR 4256
269 Campus Drive
Stanford, CA 94305-5177 


Shipping Address:

Stanford Functional Genomics Facility
CCSR Building Room 0120
1291 Welch Rd, Stanford, CA 94305-5177 


Contact Info:

Office: (650)736-1763
Lab: (650)736-2434
Fax: (650)736-2432 


8 a.m. - 6 p.m., Monday to Friday  

24/7 access for trained users




Links and Resources




Publication Acknowledgement 


As with all Stanford Service Centers, credit must be given to the Stanford Functional Genomics Facility for data that results in a publication. If the work done at SFGF produces data resulting in a figure in a publication, you are required to acknowledge the Stanford Functional Genomics Facility in the publication. Further, if SFGF staff members provided significant experimental design, data interpretation, or other intellectual contribution (as evaluated by the PI), then it is expected that these individuals will be coauthors on the publication. 


The Illumina HiSeq 4000 was purchased using a NIH S10 Shared Instrumentation Grant (S10OD018220).  Please acknowledge this grant in any publications using data from this instrument.


Return to Top



Name Role Phone Email Location
John Coller, Ph.D.
john.coller at
CCSR 0120

Price List

Search available services:
Name Description Price
Agilent Bioanalyzer - Service Work Materials Inquire
Agilent Bioanalyzer - Service Work Time (per hour) Inquire
Antibody 1 (per 10ul) - Service Work Materials Inquire
Consulting - Director (per hour) Inquire
Consulting - Technician 1 (per hour) Inquire
Custom Printing - Service Work Materials Inquire
Custom Printing - Service Work Time (per hour) Inquire
Doping Controls Commercial Batch - Service Work Materials Inquire
Gene Construct - Service Work Materials Inquire
Gene Construct - Service Work Time (per hour) Inquire
Microarray - Service Work Materials Inquire
Microarray - Service Work Time (per hour) Inquire
NGS(HiSeq) - Service Work Materials Inquire
NGS(HiSeq) - Service Work Time (per hour) Inquire
NGS(MiSeq) - Service Work Materials Inquire
NGS(MiSeq) - Service Work Time (per hour) Inquire
NGS(NextSeq) - Service Work Materials Inquire
NGS(NextSeq) - Service Work Time (per hour) Inquire
Reagents - Order Processing Fee (per order) Inquire
SFGF 24/7 Access (No Charge)

Request 24/7 access to the equipment in SFGF.