Institute for Immunity, Transplantation and Infection

The Human Immune Monitoring Center (HIMC)

For more information

Contact:

Xuhuai Ji, Genomics Manager
Email » [xuhuai.ji]

Address:
Human Immune Monitoring Center
CCSR Building, Room 0128
269 Campus Drive
Stanford, CA 94305

phone:  650-723-5050
fax:  650-498-6345

Genomics

The HIMC offers RNA and DNA extraction, Bioanalyzer services, gene expression and miRNA microarrays, and microfluidic qPCR arrays for human and mouse.

RNA and DNA extraction and quality check:  Nucleic acid extraction can be done from PAXgene RNA or DNA tubes, or from samples resuspended in Trizol.  Quality/integrity is checked using an Agilent Bioanalyzer chip (small, nano, or pico scale), which automatically determines an RNA Integrity Number (RIN) as well as a visual depiction of electrophoretic results.  The Bioanalyzer can also be used to determine total protein concentration of cell lysates of other protein samples.

Microarrays:  We offer a custom "HIMChip" microarray containing ~7000 unique probles for over 3000 human immune-related genes (click here for the list).  Genes were derived from the Immunology Database and Analysis Portal, based on the Entrez Gene, UniProt, KEGG, and various literature sources.  This is a custom Agilent SurePrint HD 8x15K format array, with 8 arrays available per slide.  We also offer whole-genome microarrays, including human and mouse miRNA arrays, on the Agilent or Illumina platform, in collaboration with the Stanford Functional Genomics Facility (SFGF).

Microfluidic qPCR arrays:  The Fluidigm BioMark system allows for the rapid construction of qPCR arrays on a microfluidic chip, using minimal samples volumes and minimal pipetting.  The system is compatible with single-cell qPCR.  A set of primers for B- and T-cell specific genes is available in the HIMC, and others can be purchased by customers for use on this platform.

User Instructions

1.  Planning your assay:  Please keep in mind the architecture of microarray chips (8 or 12 arrays per slide) when planning experiments and batches.  Please consult with us regarding optimal experimental design (1- or 2-color arrays, replicates, controls).

2.  Collecting your samples:  Good RNA quality and yield are dependent on proper sample handling.  Please see the protocols at the bottom of this page, or consult with us before delivering samples.  Avoiding sample contamination is also critical for qPCR experiments.

3.  Running your samples:  An online order is required before samples can be run. Turnaround time varies depending on the size of your project and the current workload; smaller projects can usually be completed within 3-4 weeks of order placement and sample delivery.

4.  Data analysis:  You will be notified by email when assays are completed.  Summary reports are provided for Bioanalyzer runs and microrray results.  Microarray raw data files are available for download via Dropbox, or by file transfer in the HIMC (CCSR room 0128).  Additional data analysis services are available for a fee (see our price list for details).

Protocols

Please see our Protocols page for detailed lab protocols as well as short descriptions suitable for publications and grant applications.

Addtional information:

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