Stanford Genomics

Overview of Services

Stanford Genomics provides assays, services, and access to scientific instrumentation for genomic research.  The facility is the product of combining the Genetics Sequencing Service Center (GSSC) and the Stanford Functional Genomics Facility (SFGF).   

Stanford Genomics is currently accessible and available to assist the Stanford research community with ongoing research projects as well as COVID-19 related research projects.  Please indicate in your iLab request if your project is COVID-19 related so that we can prioritize your critical and essential research.  Please contact Luisa Jimenez (luisaj@stanford.edu) or John Coller (jcoller@stanford.edu) if assistance is needed.    

Available Services: 

• High-throughput Sequencing and Library Construction utilizing Illumina NovaSeq, HiSeq 4000, NextSeq, MiSeq, and iSeq.
• 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).

• Non-Stanford Users:  Click to LOGIN with approved iLab credentials. Or, click to SIGN UP for an iLab account.

• Visit the Customer Help Manual for further guidance using iLab's Core Facility Services.

Leadership

John Coller, PhD | Stanford Genomics Service Center Director

Office: CCSR 0120  -  (650) 736-1026

Lab: CCSR 0120  -  (650) 736-2434

Email:  john.coller at stanford.edu

Staff

• Luisa Jimenez
• Alain Boussard
• Dhananjay Wagh
• Elizabeth Zuo
• Hassan Chaib
• Jason Wu
• John Coller
• Nick Addleman
• Samira Karimi
• Vanita Natu
• Vida Shokoohi
• Xuhuai Ji
• Yana Ryan

Location and Hours of Operation

Links and Resources

• Visit our (legacy) facility website for more information: http://www.microarray.org/

Publication Acknowledgement 

As with all Stanford Service Centers, credit must be given to the Stanford Genomics Service Center for data that results in a publication. If the work done at SGSC produces data resulting in a figure in a publication, you are required to acknowledge the Stanford Genomics Service Center in the publication. Further, if SGSC 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).  The Illumina  NovaSeq 6000 was also purchased using a NIH S10 Shared Instrumentation Grant (1S10OD02521201).  Please acknowledge the grant in any publications using data from these instruments.

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