# Best practices for glass back plate care and handling for Infinium HD, HTS, LCG, and XT assays

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. For best results, follow these recommendations specific for Infinium Non-EX Assays (Infinium HD, HTS, LCG and XT Assays).

**General Best Practices**

* Inspect glass back plates prior to every use. If there is any damage to the reagent reservoir or surface that faces the BeadChip, replace the glass back plate.
* Clean glass back plates according to the following schedule and protocols:
  * Before first use: **Cleaning Glass Back Plates After Every Use for Non-EX Assays**
  * After every use: **Cleaning Glass Back Plates After Every Use for Non-EX Assays**
  * After every seven uses: **Bleach Cleaning for Non-EX Assays**.

**Best Practices Updates**

* Use plastic 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 rack submerged in a container with 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 Non-EX Assays**.
* Consider the method for tracking the number of uses for each glass back plate, such as labeling the storage racks.

CAUTION: Do not write on the glass with marker as it will bleed into the array area during XStain and negatively affect the staining.

**Cleaning Glass Back Plates After Every Use for Non-EX Assays**

1. Prepare a 1% Alconox solution using 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.
4. Remove the rack from the 1% Alconox solution and thoroughly rinse the glass back plates with DI H2O.
5. Allow the glass back plates to dry in the plastic rack.
6. After the glass back plates are clean and dry, wipe them with a Kimwipe soaked with 70% EtOH.
7. Store glass back plates diagonally in the plastic rack, in a dust-free area.
8. Use a can of compressed air or a laboratory air gun to remove any dust or lint on the glass back plates before use.

**Bleach Cleaning for Non-EX Assays**\
Clean the glass back plates with bleach after approximately every seven uses, or more frequently, depending on individual lab throughput. Use the proper precautions when handling bleach, including wearing a lab coat, safety goggles, and gloves. Use the following steps to clean the glass back plates.

1. Make a 10% bleach solution.Example: Add 100 ml of standard bleach (containing 5-10% sodium hypochlorite) to 900 ml DI H2O and mix thoroughly.
2. In a fume hood, place the plastic rack with the glass back plates into the container with enough 10% bleach to cover the rack and glass back plates completely. Soak for 1 hour.
3. Transfer the plastic rack with glass back plates to a container with DI H2O.
4. Dip the rack containing the glass back plates up and down 20 times. Be careful not to chip the glass back plates.
5. Remove the rack containing the glass back plates and rinse both with DI H2O .
6. Dispose of the DI H2O from the container. Rinse and refill the container with fresh DI H2O .
7. Return the rack containing the glass back plates to the container.
8. Dip the rack containing the glass back plates up and down 20 times and then soak for 5 min. Be careful not to chip the glass back plates .
9. Repeat steps 4-7 four times.
10. Dispose of the DI H2O.
11. Remove the rack containing the glass back plates and rinse with DI H2O.
12. Allow the glass back plates to dry in the plastic rack .
13. After the glass back plates are clean and dry, wipe them with a Kimwipe soaked with 70% EtOH.
14. Store the glass back plates diagonally in the plastic rack in a dust-free area.
15. Use a can of compressed air or a laboratory air gun to remove any dust or lint on the glass back plates before use.

For additional information, refer to [Infinium Lab Setup & Best Practices](https://support.illumina.com/downloads/infinium-assay-lab-setup-and-procedures-11322460.html) .

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #1421), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001421%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000001421.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.