Sam:LabNotes/Microbiome/2009-2-12

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Test of Microwell Slide Washing and Microbeads Loading[edit]

Objective[edit]

  • Clean and sterilize the slides before beads loading.
  • Load the bead on slides and evaluating the slide quality, bead arrangement under microscope.



Slide washing[edit]

Reagents[edit]

  • 1N HCL (diluted from 12N to 1N)
  • Acetone
  • Ethanol (200-proof)
  • 1X PBS


Procedures[edit]

  • Prepare several cleaned tip-box caps by following wash: 100% EtOH rinse + di-H2O rinse, repeat once.
  • Fill up the wash reagents into the caps. Label the box accordingly.
  • Soak the slides in different reagents and gentle agitation. Rinse the slide twice with diH2O in between. Time the soaking time and observe the change of slide.


Results[edit]

  • The slide can not resist to either Acetone or Ethanol soaking. The array piece peeled off by itself after 30 sec-40 sec of soaking.
  • The slide can resist to 1N HCL soaking (> 1 min) without noticeable change of property.


Revised washing steps[edit]

  • 1N HCL, 1 min -> 1st di-H2O, 1 min ->, 2nd di-H2O -> 1X PBS, 1 min -> dry up in fume hood, 5 - 10 min.
    • The 1N KOH wasn't used to neutralize 1N HCL since the KOH residue may remain and interfere the downstream application such PCR reaction.



Microbead loading[edit]

Procedures[edit]

  • Start from the diluted and immobilized bead (with FITC labeled probes). Concentration: 1 mg/200 uL.


  • Resuspend by repeat pipetting using p200 pipettor.
  • Dilute in 1/200 ratio with nuclease-free H2O
    • Take 1 uL resuspension into a fresh 1.5 mL tube with 199 uL Nuclease-free H2O. Mix gently by repeat pipetting (p200).
    • The new bead conc. will be 6 x 10^7 bead / 200 (uL) x 1/200 = 1500 bead /uL


  • Leave the slide on Magnetic board. Transfer 10 uL, 20 uL, 40 uL on microwell arrays.
    • The bead drop can barely cover the entire array area except using 20 ~ 40 uL of total volume.


  • Air day the slides in fume hood until all of the diluent are fully evaporated (More than 10 min will be needed to dry up)
    • It may be possible to dry on on magnetic hot plate at 60 degree.

Microscope images[edit]

  • The structure microwell and microbead were characterized using Zessis A1-mode fluorescent microscope with 10X objective


FIG. 1: Black and white image (10X objective)


FIG. 2: Color image in green (10X objective)


Discussion[edit]

  • No bead was found on microwell arrays in both B&W and color images. It is possible that:
  1. beads floated around on magnetic hot plate. The hot plate can't attract beads with enough magnetic force.
  2. The dilution of bead is not optimized ideally.


  • Still some dust could be found on microwell arrays.
  1. Higher conc. of HCL or longer soaking time could be applied in more tests in the furture.