Test Drive: Organoid Serial Passage Workflow Chain

💡 Tip: Add your name as a prefix to each experiment you createBecause there may be several users logged into the same L7|ESP instance, prefix each experiment name with your name or initials (e.g. JD_OrganoidPassage_P1) so you can quickly identify your own work.
1) Set Up the Experiment
  • From the homepage, navigate to Projects
  • Open the Organoids project
  • Click Experiment → select Workflow Chain
  • Choose Organoid Serial Passage Chain from the list and confirm the latest version is selected
  • Enter a name for the experiment, prefixed with your name (e.g. JD_OrganoidPassage_P1), then click Next
  • Confirm the Organoid Cell Passage workflow is shown as the start node and click NextNote: For this single-workflow chain the start node is selected automatically. More complex chains may offer multiple starting points.
2) Add a New Organoid Line Entity
  • Click Add New Entity — the entity type is automatically restricted to Organoid Line
  • Fill in the entity fields:
    • Tissue Source— enter the relevant tissue source
    • Donor ID— enter the donor identifier
    • Passage Number— typically0or1
    • Passage Date— can be set to a past date for testing purposes
  • Click Next, then click Save and Submit to queue the experimentNote: Alternatively, choose Save, Submit, and Create Worksheet to bypass the LIMS queue and go directly to the worksheet — useful when you are the sole operator.
  • On the confirmation dialog, click Submit Entities
3) Execute the Workflow in LIMS
  • Navigate to LIMS and locate the queued experiment — click Add WorksheetNote: Use the filter to narrow results to your own entries if multiple users are active. The list refreshes in real time.
  • Open the worksheet and choose your preferred view: Standard or TransposedNote: Shared fields at the top apply to all samples (e.g. date, microscope). Per-entity fields are completed individually for each sample. Fields shown in grey are read-only, populated automatically from existing records or calculations.
4) Complete the 6 Workflow Steps
  • Step 1 — Pre-Passage Assessment
  • Enter today's date in the shared date field
  • Select the Microscope Used from the pre-filtered equipment list
  • Fill in any additional shared or per-entity fields as required, then click Complete → Save and Continue
  • Step 2 — Dissolution
  • Select the Centrifuge from the equipment usage panel and review its displayed maintenance and calibration status
  • Enter the Cold Buffer Volume (in mL) for each organoid line individually, or configure it as a shared field if all samples use the same volume
  • Complete any remaining drop-down selections, then click Save and Continue
  • Step 3 — Harvesting / Dissociation
  • Select the Dissociation Route — this is a mandatory field (marked with a red asterisk)Note: Choose Single Cell or Mechanical as appropriate. Different routes may expose different downstream fields.
  • If Single Cell is selected, double-click the Dissociation Enzymes field and choose from the controlled list
  • Optionally set Target Fragment Size and Quality, then click Save and Continue
  • Step 4 — Cell Counting (single-cell route)
  • Select the Cell Counter from the equipment panel
  • Enter the Total Cell Count and Live Cell Count — viability will be calculated automatically
  • Enter the Sample Volume to calculate total cells availableNote: Calculated fields may be editable or read-only depending on your system configuration.
  • Click Complete → Save and Continue
  • Step 5 — Re-Embedding / New Culture Setup
  • Enter the Dome Count (number of new cultures to create) — valid range is 1–7, default is 1Note: The dome count entered here determines how many new organoid line entities are generated in the next step.
  • Click Save — the split ratio will be calculated automatically
  • Optionally select a Plate Format and specify Matrigel Volume and Incubator, then click Save and Continue
  • Step 6 — New Passage Entity Creation
  • The system automatically creates the number of new child organoid line entities specified by the dome count — each will show the parent entity ID
  • Enter the Passage Date for the new cultures
  • In the Next Workflow field, double-click and select Organoid Cell Passage for each entity you want to continue passaging — leave blank for any line you wish to stopNote: You can configure this field to be driven automatically by business logic — for example, stopping progression if a quality check fails.
5) Submit and Loop to the Next Passage
  • Click Complete → Save — at the end of the final step you will see a Submit to Next Workflow button
  • Click Submit to Next Workflow — the system automatically creates a new experiment containing only the entities you marked to continue (the count is shown in brackets)
  • Return to LIMS, locate the newly queued experiment, give it an updated name (e.g. JD_OrganoidPassage_P2), then click Add Worksheet
  • Repeat Sections 3 and 4 to complete the next passage round — previous viability and days-since-last-passage values will be pre-populated from the prior roundNote: This loop can be repeated indefinitely. Each new passage round generates a fresh set of child entities linked back to their parent.