XStain glass back plate care recommendations for Infinium EX Assays

NOTE: This article contains glass back plate recommendations which are applicable to Infinium EX format BeadChips only. For legacy Infinium assays (HD Super, HD Ultra, HD Methylation, HTS, LCG, LCG Quad, XT), refer to article Improve Infinium data with these updated XStain glass back plate care recommendations.

Call rates and Log R Dev for Infinium BeadChips are calculated using signal intensities that rely on effective staining across the BeadChip. Glass back plates are a key component of the flow-through chambers that control the flow of XStain reagents over Infinium BeadChips. Careful cleaning and handling of glass back plates is critical for the quality of the XStain procedure. Follow these updated recommendations for Infinium EX Assay for best results.

Best practices

• Inspect glass back plates prior to every use to make sure they are in acceptable condition. Replace the glass back plate if any of the following are observed:

  • Chips or damage in the reagent reservoir area or on the surface facing the BeadChip in the flow-through chamber

  • Cracks in the glass that may cause the glass to break during the assay

  • Chips or damage that may cause harm while handled, regardless of location

• Use a plastic (polypropylene) test tube rack (Cole-Parmer Item # EW-06739-17) for cleaning, bleaching, and storage of glass back plates. Place glass back plates diagonally in the racks to minimize contact between the glass and to prevent damage.

• Immediately after the XStain procedure, disassemble flow-through chambers and place the glass back plates diagonally in a plastic test tube rack submerged in a container of DI H2O to prevent XStain reagents from drying on the glass back plates. Keep glass back plates submerged in DI H2O until ready to proceed to Cleaning Glass Back Plates After Every Use for EX Assays.

• Consider your method for tracking the number of uses for each glass back plate, such as labeling the storage racks. CAUTION: if you write on the glass with marker, it will bleed into the array area during XStain and negatively affect the staining.

Clean glass back plates according to the following schedule and protocols:

• • Before the first use: Bleach Cleaning Glass Back Plates for EX Assays.

  • After every use: Cleaning Glass Back Plates After Every Use for EX Assays.

  • Before every use: Bleach Cleaning Glass Back Plates for EX Assays.

Cleaning Glass Back Plates After Every Use for EX Assays If using new glass back plates, proceed directly to Bleach Cleaning Glass Back Plates for EX Assays.

1. Prepare a 1% Alconox solution. Use 2.5 g Alconox powder per 250 ml DI H2O.

2. Submerge the plastic rack with glass back plates in a container filled with 1% Alconox.

3. Wipe each glass back plate with a Kimwipe and return to rack. Leave overnight.

4. Remove glass back plates from the 1% Alconox solution and thoroughly rinse the glass back plates with DI H2O.

5. After Alconox cleaning, the glass back plates can be stored diagonally in the plastic test tube rack to prevent damage. Before use, perform Bleach Cleaning Glass Back Plates for EX Assays.

Bleach Cleaning Glass Back Plates for EX Assays Use the proper precautions when handling bleach, including wearing a lab coat, safety goggles, and gloves.

Important: Clean the XCG glass back plates as outlined in steps 1 through 4 with soaking taking place overnight or 1-2 hours before use.

1. Prepare a bleach solution with a final sodium hypochlorite concentration of 0.5-1.0%. Use bleach with a starting sodium hypochlorite solution of 5-10%, and then dilute 10-fold with DI H2O. For example, if using 100 ml of a bleach solution originally containing 8% sodium hypochlorite, add 900 ml of DI H20 to obtain acceptable final sodium hypochlorite concentration of 0.8%.

2. Submerge the plastic rack with glass back plates in a container filled with 1% bleach solution and soak for 1 hour or overnight.

3. Remove glass back plates from the 1% bleach solution and thoroughly rinse the glass back plates with DI H2O.

4. Wipe the glass back plates with a Kimwipe soaked with 70% EtOH.

5. After bleach cleaning, the glass back plates can be placed diagonally in a plastic test tube rack in the interim period before use.

Refer to the Infinium Lab Setup & Best Practices: Infinium Assay Best Practices, sub-section "Glass Back Plates" for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #8440), contact Illumina Technical Support [e-mail].