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How do I order custom panels for Targeted Gene Expression from 10x Compatible Partners?

Question: How do I order custom panels for Targeted Gene Expression from 10x Compatible Partners?

Answer: For the Targeted Gene Expression assay, after designing custom panels using the 10x Genomics Custom Panel Designer, panels can be purchased as 5’-biotinylated oligo pools from the 10x Genomics Compatible Partner, Integrated DNA Technologies, Inc. (IDT), as described in detail below. IDT panels are supported for use as add-on or fully custom panels in Single Cell Targeted assay, and as add-on panels in the Spatial Targeted assay. 

Fully custom panels for use in the Single Cell Targeted assay can also be generated by following our Demonstrated Protocol CG000412 for biotinylation and amplification of Twist Oligo Pools.

Furthermore, it may be possible to order panels from other vendors, as described here. However, panels from alternative vendors have not been validated for use with the Targeted Gene Expression assay and are not officially supported by 10x Genomics. Assay performance cannot be guaranteed when working with untested panel formats.

IDT panel formats

IDT synthesizes custom panels in two different formats that have been tested by 10x Genomics: NGS Discovery Pools and xGenTM LockdownTM Probe Pools.  Both panel formats are officially supported by 10x Genomics for use as fully custom panels or add-ons to the 10x pre-designed panels in the Targeted Gene Expression assay. 

Selecting the appropriate IDT panel format for the application is important for optimal results and for minimizing cost:

  • NGS Discovery Pools are appropriate for many research applications. They provide a fast turnaround time (~5 days for pools <50k baits) and a low per-bait cost. The data described in our Technical Note on custom panel performance were generated using NGS Discovery Pools.
  • Some researchers may be running studies that require a higher degree of quality control. For these applications, we recommend IDT's xGenTM LockdownTM Probe Pools, which undergo additional per-bait quality control after synthesis. These panels have a higher cost and longer turnaround time (7-10 business days for orders <2000 baits).

Steps for designing and ordering custom panels from IDT:

1. Use the 10x Genomics Custom Panel Designer to generate a “Bait Design file” (.xlsx) for a fully custom panel or add-on panel.

  • This file has a three-column format, with one line per bait:
    • table_3_column.png

2. Upload the Bait Design File (.xlsx) to IDT’s website. This can be achieved by selecting “order my design” on the NGS Discovery Pools page or the xGenTM LockdownTM Probe Pools page.

  • If ordering NGS Discovery Pools, the Bait Design file (.xlsx) can be uploaded without modification.
  • If ordering xGenTM LockdownTM Probe Pools, the format of the Bait Design file requires modification before uploading. Column A (“Pool Name”)  in the Bait Design file should be deleted and replaced with column C (“Bait ID”). Column B (“Sequence”) should be left unchanged. This will result in a final file with two columns (Bait ID, Sequence), as in this example:
    • table_2_column.png
  • Custom panels can be purchased in 16 rxn (64 µl) and 96 rxn (384 µl) formats. The volume of custom panel needed per targeted assay will depend on the number of baits in the custom panel, and whether it is used as an add-on or fully custom panel. Please refer to the Targeted Gene Expression User Guide for more information.

3. Place an order with IDT

4. After receiving the custom panels from IDT, store them at -20 °C until use. 

5. Perform the targeted assay by following the Targeted Gene Expression User Guide.

  • Please refer to the “panel dilution guidelines” for step 2.1 to dilute the custom panel to an appropriate working dilution in 1X TE buffer, which can be purchased from IDT (#11-05-01-13)

Note on ordering add-on panels with fewer than 50 baits:

Please note that the minimum number of baits per order is 50. When purchasing custom panels with fewer than 50 baits, we recommend replicating the entire design as many times as necessary to reach the 50 bait minimum. For example, for a custom panel containing 18 baits, each bait can be duplicated three times for a total panel size of 54 baits. When using these small custom panels as add-on panels with 10x pre-designed panels, this duplication factor will be used when diluting the custom panel to a working concentration, following the protocol provided in the Targeted Gene Expression User Guide.

Product: Targeted Gene Expression