Array Advice - Washing Slides

 

View tips and solutions to common problems for washing array slides:

Tips

  • Ensure wash dishes are cleaned with appropriate solvent and are free of fluorescence. Washing should be done after every array processing run and monitoring the background signal intensity from each run will give an indication if there is an issue.
  • The correct volume of wash buffer 2 and wash dish 2 should be prewarmed at 37°C, ideally overnight.
  • Droplets of buffer still present on slide after washing will result in artefacts on tiff image.

 

Solutions to common problems

Problem 1 – Fluorescent smears across slide

Fig 1. Fluorescent smears across slide

Figure 1. Fluorescent smears across slide

Causes:

  1. Contamination with fluorescent material during washing
  2. Arrays have dried out during hybridisation or wash

Solutions:

  1. Wear clean gloves
  2. Ensure forceps are cleaned with MQ water before and between washes
  3. Wash slide with acetonitrile (toxic!) for 1 min at room temperature
  4. Wash dishes with acetonitrile to remove buildup of unincorporated dyes, or replace dishes
  5. Separate slide from sandwich while submerged in wash buffer 1

 

Problem 2 – Artefact on array

Fig. 2. Artefact on array due to wash buffer droplets on the slideFigure 2. Artefact on array due to wash buffer droplets on the slide

Causes: Dried wash buffer droplets on the slide

Solution: Ensure the slide is removed very slowly from wash buffer 2 to prevent droplets from remaining on slide

 

Problem 3 – High background noise

Fig 3. High background noiseFigure 3. High background noise

Causes:

  1. Wash conditions not stringent enough.
  2. Contamination with fluorescent material during wash.

Solutions:

  1. Wear clean gloves
  2. Ensure forceps are cleaned with MQ water before and between washes.
  3. Wash dishes with acetonitrile to remove buildup of unincorporated dyes, or replace dishes.
  4. Ensure magnet produces a vortex in wash solution prior to adding slides.

 

CytoSure™ products are for research use only; not for use in diagnostic procedures