DPL-980 Import PBMC tubes into Sequencescape

[KatyTaylor]

User story As a member of the SSR team, who has received tubes from faculty containing PBMCs, I would like to be able to import them into Sequencescape along with all the required data.

Acceptance Criteria

• [ ] Purpose name should be "LRC Bank Input"
• [ ] Add to documentation that it's possible that these samples could already be in the system, having been imported into the system as fresh blood. They will be represented as different samples in the system (new 'sanger sample id'), but have the same supplier sample name, which could be used to link them up in reporting if needed. In fact this is true across all the different entry points in the pipeline.

Outstanding questions for stakeholders

1. Can we use the existing "scRNA Core" manifest to import these tubes? It includes the following columns:
   • Tube barcode
   • Sanger sample ID (assigned by Sequencescape)
   • Collection site
   • Donor ID
   • Supplier name - populated with Vac tube barcode
   • Volume
   • Retention instruction

Additional information

The samples might exist in Sequencescape already (because they could stem from samples that arrived on site as fresh blood, were imported into Sequencescape as "LRC Blood Vac" tubes, then an aliquot taken, and returned to faculty). Elsewhere in Sequencescape, this is handled by importing it as a new 'sample' in Sequencescape but it would have the same Supplier Name (= Vac tube barcode).

We've agreed to follow this same pattern here. An alternative strategy of automatically linking up to the old sample on manifest upload (using the supplier sample name) was considered but felt to be unsafe due to the possibilities that:

• there could be unrelated samples in the db with the same supplier sample name
• samples supplied as PBMC tubes could theoretically be sequenced under a different study to the same sample supplied earlier as fresh blood - easier in this case if they are represented as different samples in the system.

[KatyTaylor]

Was agreed this was not urgent and could be done in 'Phase 3'.

[KatyTaylor]

This has now been requested to be brought forward into Phase 2.

[yoldas]

The story #4159 already adds the required LRC. Bank Input Sequencescape purpose record and adds integration suite for submitting them together with Seq/Spare tubes.

The following documentation sections are added/updated: Importing faculty PBMC tubes, Submitting faculty PBMC tubes for Donor Pooling and cDNA Prep, and Submitting banked PBMC tubes for Donor Pooling and cDNA Prep.