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Extended Throughput Kit v1.1

The Extended Throughput Kit v1.1 enables processing of additional PCR plates, each with the same set of 96 i5-index sequences but a different i7 index pool (RNA-A-AP1 to RNA-A-AP4). This allows for higher throughput by analyzing each plate as a separate fastq library and then merging outputs at the single-cell level.

Cells from different plates are distinguished by appending the library name (P7 primer pool) to the cell barcode in the gene expression matrix outputs.

Single Sequencing Run

If all plates are sequenced together in the same run, you can analyze them in a single Nextflow run:

  1. Create a sample barcode table for all plates and samples:
    • List each sample on each plate (repeat the sample name for each plate used)
    • Set the libIndex column to the name of the barcode pool (e.g., RNA-A-AP1)
    • See sample-barcode-table example
  2. Launch the workflow: bash nextflow run /PATH/TO/ScaleRna -profile PROFILE -params-file /PATH/TO/ScaleRna/docs/examples/extended-throughput/runParams.yml --outDir output.ext
    • This will produce outputs for each individual plate as well as merged outputs (with default merge set), combining all cells for each sample across all plates
  3. Outputs:
    • Individual outputs for each plate
    • Merged outputs for each sample across all plates (default merge enabled)

Merging Across Multiple Runs

See Merging Multiple Runs for instructions on merging data from separate sequencing runs or plates.

Fastq Generation

To start from fastq files instead of a BCL run folder, see Sequencing Reads & Fastq Generation.

Need Help?

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