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Create a 3' Transcriptome custom design

Build and publish a Cytos™ 3' Transcriptome design in Custom Designer.

Create the design​

  1. On the Custom Designer page, select Start a Design.
  2. Enter a unique name and, optionally, a description.
  3. Under Configure your Cytos Workflow, toggle RNA to add RNA detection, and then select 3' Transcriptome.
  4. If including protein, toggle Protein on to add protein detection.
  5. Select Customize Modules to begin your design.
  6. Review the cell paint module, and then select Next.
  7. If you added protein detection, build your protein panel. See Build a protein panel.
  8. Review the 3' Transcriptome batch settings. Custom Designer determines the batches and cycles per batch automatically.
  9. Select Finalize Design, and then review the design package summary.
  10. Select Save as Draft, or on the Design Package Preview page, select Publish Design.

    Only published designs can be used in a planned run or manual run on the instrument.

Build a protein panel​

A design that includes protein detection captures protein expression alongside the other modalities in the design. Build the panel from Cytos Fixed Protein Panels, your own custom targets, or both, up to a maximum of 20 protein targets.

  1. Select the protein module.
  2. Add targets from either source, or from both:
    • Cytos Fixed Protein Panels: Select any combination of panels. Each panel consumes four of your 20 total targets. See the Cytos Protein Panel Targets (MA-00099) for the protein targets in each panel.
    • Custom Protein Targets: Enter names manually with one protein per line, paste from Excel, or upload a CSV file. For custom protein naming rules and example inputs, see Format custom protein targets.
  3. Select Next.
Note:

You are responsible for providing the primary antibodies for custom proteins.

Caution:

Fluorescent reporter cell lines are not recommended. Fluorescent reporters can interfere with Cytos imaging and might reduce image quality or affect downstream results. Element does not recommend or support workflows that use fluorescent reporter cell lines.

Format custom protein targets​

Custom protein targets that are part of custom designs must meet the following specifications:

  • Protein names can include up to 64 letters (A-Z, a-z), numbers (0-9), dash, dot, parentheses, and underscores. Do not include spaces.
  • For manual entry, separate protein names with a new line, paste from Excel, or upload the protein names in a CSV file format.

The following names are examples of custom protein targets:

phos-ATM
Plk1
phosS32-cFos
phosS78-HSP27
Rb
cFOS
JNK123

Manage your design​

To edit, clone, download, or delete a design after you create it, see Custom Designer.

See also​

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