9  Appendix A: Supplies and Reagents

This appendix provides a consolidated checklist of supplies and reagents used across Modules 1 through 8.

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9.1 Core Supplies and Equipment

  • Disposable lab coats, nitrile gloves, and safety goggles
  • Benchtop disinfectant (70% ethanol)
  • Micropipettes (single channel and multichannel)
  • Sterile pipette tips (appropriate volumes, preferably filtered)
  • Sterile reservoirs for multichannel loading
  • Sterile microcentrifuge tubes and culture tubes
  • DNA LoBind 1.5 ml microfuge tubes (Eppendorf)
  • Centrifuge and microcentrifuge
  • Vortex mixer
  • Shaking incubator for 30°C and 33°C incubation
  • Incubator for 30-33°C static cultures and plates
  • 96-well microplates
  • Breathe-Easy breathable plate seals
  • Peg-lid biofilm assay plates
  • Cerillo Duet co-culture plate system
  • Plate reader (OD600 kinetic and endpoint absorbance)
  • Invitrogen Qubit fluorometer and assay tubes
  • Invitrogen Qubit dsDNA HS Assay Kit
  • Turbidimeter (Biolog Turbidimeter or equivalent)
  • Sterile loops for colony transfer
  • Biohazard waste containers

9.2 Microbiology Media and Biological Materials

  • Delftia acidovorans isolates and comparison isolates
  • Tryptic Soy Agar (TSA) plates (Teknova or Hardy Diagnostics))
  • Tryptic Soy Broth (TSB) for liquid cultures (Teknova or Hardy Diagnostics)
  • Biolog Blood Universal Growth (BUG) agar
  • Biolog GEN III Microplates
  • Biolog IF-A inoculating fluid (for Biolog GEN III assays)
  • Phosphate-buffered saline (PBS)

9.3 Reagents for Pipetting and Assay Setup

  • MiniPCR micropipetting cards
  • Crystal violet solution (serial dilution activity)
  • Dyed water solutions (blue, yellow, red food coloring) for volume challenge
  • Dojindo biofilm viability detection reagent components:
    • WST solution
    • Electron mediator reagent
    • TSB diluent

9.4 DNA Extraction and Sequencing Reagents

  • TE buffer (Ambion)
  • Sigma Lysozyme (10 mg/mL in TE; powder form stored at -80°C)
  • New England Biolabs (NEB) Monarch Proteinase K
  • New England Biolabs (NEB) Monarch RNase A
  • CTAB buffer (Promega)
  • New England Biolabs (NEB) Monarch gDNA Binding Buffer
  • New England Biolabs (NEB) Monarch wash buffers
  • New England Biolabs (NEB) Monarch gDNA Elution Buffer
  • Oxford Nanopore Technologies (ONT) Rapid Barcoding Kit (SQK-RBK114.24)reagents
  • ONT Flow Cells (FLO-MIN114) and associated reagents for sequencing runs

9.5 Computational and Data Resources

  • Electronic lab notebook (ELN)
  • Quarto for workbook rendering
  • BV-BRC.org account and workspace for assembly and annotation workflows
  • SeqHub.org for genome exploration

9.6 Notes

  • Prepare all sterile materials in advance and confirm lot numbers where required.
  • Record any reagent substitutions, concentration changes, or protocol deviations in the ELN.
  • Follow institutional biosafety and chemical safety policies at all times.