> Wanunu Lab SOPs, protocols, and tutorials

This page links to Standard Operating Procedures (SOPs), Protocols, Tutorials, and other documents critical to the operations in the lab. Please refer to these documents and update as needed.


Disclaimer: All the documents and information in this Wiki series are prepared as a reference for the members of the Wanunu Lab at Northeastern University. Usage and sharing by third-party laboratories without permission is not advised. All processes and operations are intended for internal usage only, and may not be suitable for other laboratories.

For modifications, addition of new pages, etc. contact the website manager (Ali Fallahi, as of 2021).

Standard Operating Procedures

Standard Operating Procedures are documents that enclose critical instructions to safely and successfully conduct an experiment, operate a device, or handle a chemical or biological agent. SOPs include summaries of what the process does, how to do it, what the hazards are, and how to manage waste, accidents or failures. It is mandatory for the members of our lab to carefully read and understand the SOPs and subsequently be trained on the process in person by the PI or another designated individual. Official SOPs include the names of all individuals who have completed the training and demonstrated their ability to perform the tasks associated with the SOP.

Chemical SOPs

  • Inorganic Chemicals

    • Piranha Etch : Concentrated Sulfuric Acid and Hydrogen Peroxide
    • Buffered Oxide Etch (BOE) : 6-to-1 hydrofluoric acid (HF), ammonium fluoride, and surfactant
    • Potassium Hydroxide Etch: Heated 30% KOH bath
    • Metal Etchants (Chromium, Gold, Aluminum, etc.)
    • Gases and Tanks (Oxygen, Ozone, Nitrogen, Hydrogen, Sulfur Hexafluoride, Argon)
    • Liquid Nitrogen tanks
  • Organic Chemicals

    • Photoresists and associated developers and solvents
    • Organo-silanes
    • Organic acids


Biological SOPs

  • Live agents

    • E-coli bacterial lines
  • Recombinant nucleic acids or proteins

    • Plasmids (for transfection)
    • Sequencing or nanopore experiment samples

Device SOPs

  • Microscopes

    • Transmission Electron Microscope (TEM)
    • Scanning Electron Microscope (SEM) and E-beam Lithography
    • Atomic Force Microscope (AFM)
    • Optical microscopes around the lab
  • Biomaterials and reagent preparation

    • Autoclave
    • HPLC
    • Gel elecrophoresis and gel scanner
    • Rotary evaporator
    • pH and conductivity meter
    • Refridgeration (4 °C, -20 °C. -80 °C) and chemical cabinets
    • Glovebox
  • Fabrication

    • Sputter Coater
    • Mask Aligner (Karl Suss MA6)
    • Plasma cleaner/etch (Reactive Ion Etch)
    • Chemical vapor deposition (CVD)
    • Atomic Layer Deposition (ALD)
    • Ellipsometer
  • Prototyping, electronics

    • Formlabs Form2 SLA resin printer
    • Laser cutter
    • the blade cutter thing?
    • Drill press
    • Soldering stations
    • Sheet resistance measurement device
  • Experimental Setups

    • Axopatch 200B stations (Egan 331A)
    • Photothermal membrane etching station (Egan 331)
    • ZMW sequencing setup with TURF microscopy (Egan 331)
    • ZMW TURF microscopy station (Egan 331A)
    • Chimera high-bandwidth stations
    • Water desalination station
  • Other

    • Please list other SOPs and documents



Common protocols for conducting processes in the lab are listed below. Protocols include detailed step-by-step walkthrough of a process, expected intermediate tests and results, as well as examples of successful and failed final results. To reduce redundancy and duplicates, protocols must be as cross-referenced with one-another and with SOPs as possible.

  • Chip and pore fabrication

    • Free-standing SiNx membrane (SiNx, SiO2, <100> Si, SiO2, SiNx wafer)
    • SU-8 pillar chip (single channel Si)
    • SU-8 pillar optical chip (4-channel on fused silica)
    • eZMW chips
    • MoS2 freestanding membrane
    • TEM pore drilling
    • ALD coating on wafers and chips
    • Small feature formation in sputter-coated fused silica
  • Chip Cleaning

    • Piranha cleaning of free-standing SiNx membrane chips
    • Plasma cleaning of free-standing SiNx membrane chips
    • Plasma cleaning of SU-8 pillar chips
    • Plasma cleaning of ZMW chips
  • Buffer preparation

    • List your buffers here
  • Lipid / Polymer Membranes

    • DPhPc
    • Polymer membrane
    • Vesicles
  • Chemical modifications of solid surfaces

    • PEG-silanes
    • Other silaneshttps://wanunu.sites.northeastern.edu/wiki/wanunu-lab-sops-manuals-and-tutorials/lab-github-usage-for-posting-code-and-analysis/
    • Polyvinyl Phosphonic Acid (PVPA)
    • add your other surface modifications here
  • Experimental protocols

    • List your experiment’s protocols here


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