Protocol Library

Welcome

This site hosts the standardised protocol library for the lab, including buffers, mouse and human workflows, flow panels, and general methods. All documents follow a common Quarto template and are versioned.

Use the navigation bar on the left to browse by category or search for a protocol by name.

How to use this library

  • Browse by category using the sidebar:

    • Buffers – all stock and working solutions.
    • Mouse – mouse tissue processing and functional assays.
    • Human – human PBMC and cell line protocols.
    • General – cross-cutting methods (e.g. flow staining, nucleofection).

  • Download as PDF
    Each protocol page includes a PDF version suitable for printing or attaching to experiment documentation.

  • Search
    Use the search box in the sidebar to find protocols by keyword (e.g. “liver digestion”, “PBMC”, “ACK lysis”).

Naming and versioning conventions

Protocols and buffers follow a consistent naming scheme:

  • Buffers: buf_<target>_vX.Y, e.g. buf_liver_digestion_v1.0
  • Mouse protocols: prot_mus_<tissue_or_process>_vX.Y
  • Human protocols: prot_hum_<tissue_or_process>_vX.Y
  • General protocols: prot_gen_<process>_vX.Y

Version numbers are incremented when the procedure changes in a way that could affect results (reagent changes, timings, etc.).

The title and version in each protocol’s YAML header define what appears on the website and in the PDF.

Document structure

Most protocols follow a common structure:

  1. Purpose and scope – what the protocol is for and when to use it.
  2. Reagents and materials – linked to buffer entries where applicable.
  3. Equipment – key instruments and settings.
  4. Procedure – stepwise instructions.
  5. Notes and troubleshooting – optional recommendations, pitfalls, or variants.

Buffers have a simplified structure focusing on:

  • Composition (final concentrations)
  • Preparation steps
  • Storage and stability
  • Safety considerations