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ScalePlex

Overview

ScalePlex enables higher sample multiplexing by labeling cells during fixation before loading onto the RT plate. This allows you to pool multiple samples together and later assign cells back to their original samples.

How ScalePlex Works

  • Dual Oligo System: Each well of the ScalePlex Oligo Plate contains two oligos:

    • Row-specific oligo: Unique to each row (A-H)
    • Column-specific oligo: Unique to each column (1-12)
    • Combination: The intersection creates a unique identifier for each well

  • Sample Pooling Process:

    1. Cells are labeled with ScalePlex oligos during fixation
    2. Labeled cells from multiple samples are pooled together
    3. Pool is loaded into RT plate wells
    4. After sequencing, cells are assigned back to original samples using oligo combinations

ScalePlex Pool as a "Sample"

A ScalePlex pool (biological samples fixed on one ScalePlex fixation plate) is treated as a single "sample" in the pipeline. Cell calling occurs on the entire pool first, then the ScalePlex workflow assigns cells to their original fixation plates. The Sample Report Summary tab shows metrics for the entire pool, while the ScalePlex tab provides detailed deconvolution results. For detailed information about ScalePlex outputs, reporting and analysis, here

Supported Versions

  • ScaleBio Seq Suite RNA v1.6+: Basic ScalePlex support
  • ScaleRNA v2.0+: Full QuantumScale compatibility
  • Extended Throughput: Compatible with multi-plate workflows

Outputs

  • After processing, cells are assigned back to their original samples using the ScalePlex oligo combinations.
  • Key output files include per-cell assignments that can be used in downstream analysis.

For details on analysis methods, cell assignment algorithms, quality control, and troubleshooting, see ScalePlex Analysis.

Need Help?

For more information, please contact support@scale.bio or visit our support website.