3 keys to obtain high quality microarray results consistently

  1. Purity of cells
  2. Purity of RNA
  3. Processed by same protocol, same person, same facility

RNA extraction and purification using Trizol + clean-up kit for small number of cells (2000~50000 cells)

Reagents needed
  • Qiagen RNeasy minelute cleanup kit
  • Trizol
  • Chloroform
  • RNA quality 70% EtOH
  • RNA quality 80% EtOH
  • RNase free eppendorf tubes, filter tips
  1. Sort cells directly into 1000 µL Trizol in RNase free eppendorf tube.
  2. Mix briefly after sort.
  3. Store at -80°C.
RNA extraction and purification
  1. Thaw trizol-sorted cells on ice.
  2. Add 200 µL Chloroform, mix vigorously for 15 seconds.
  3. Keep on ice 10 min, spin 15 min at max speed at 4°C.
  4. Transfer 450 µL aqueous phase (carefully) to new, clean tube. Do not disrupt interphase by inserting tip deeper or making turbulent flow. (tip: set P200 pipetter at 150 µL and pipette up 150µL three times)
  5. Add 450 µL RNA quality 70% EtOH, mix thoroughly by pipette.
  6. Transfer 700 µL to RNeasy MinElute spin column. Spin 15 sec at 8000x g at RT (room temperature).
  7. Dump flow-through. Add rest of sample to spin column. Spin 15 sec at 8000x g at RT. (tip: aspirate flow-through instead of pouring to prevent waste from getting on lip of tube)
  8. Dump flow-through. Transfer column to new clean tube. Add 500 µL RPE buffer (provided by MiniElute kit). Spin 15 sec at 8000x g at RT. (tip: optional to switch to clean tube. The kit doesn’t supply enough waste tubes for this step)
  9. Dump flow-through. Add 500 µL of RNA quality 80% EtOH. Spin 2 min at 8000x g at RT.
  10. Dump flow-through. Transfer column to new tube.
  11. Open lid of column, spin 5 min at max speed at RT to dry.
  12. Discard tube. Transfer to 1.5 mL collection tube.
  13. Add 14 µL RNase-free water directly to column membrane. Spin 1 min at full speed at RT. Final volume will be around 12 µL.
  14. Store RNA at -80°C until submission to microarray core facility for two-round amplification and following processes.

Gene Expression Microarray Sample Processing

Stanford University PAN(Protein and Nucleic Acid) Facility Gene Expression Core

Stanford University PAN Facility Gene Expression Core provides full service for Affymetrix type microarray for both on-campus and off-campus researchers. Two-round amplification protocol based on Affymetrix protocol is available.

Please contact Elizabeth Zuo for further questions and pricing.

  • Stanford PAN Facility Gene Expression Core
  • Phone: (650) 723-3328 or (650) 724-0768
  • Email:
  • Address: Stanford PAN Facility
    279 Campus Drive West
    Beckman Center, Room B065 or B017
    Stanford, CA 94305