General Lab Protocols

Washing Dishes

Notes

  • Do NOT use the sink located by the LCMS instruments.
  • Do NOT use soap to wash any glassware in the lab. It can interfere with fatty acid and lipid analyses on the LCMS. If you require soap, keep that glassware separate from the general lab glassware.
  • The procedure for washing glassware used for bacterial culture only applies to organisms classified as BSL2 and lower (e.g., engineered organisms, Pseudomonas species, etc.)
  • Glassware can be dried on the drying racks located above the sinks or in the drying oven located in the hall across the graduate/post-doc office.

Procedure:

For glassware used for bacterial cultures:

  1. Wash glassware at the sink labeled “Bacterial Wash Station.”
  2. Find a plastic or glass receptacle and dump your cultures in the container.
  3. Add bleach to the culture to a final concentration of 10%. Let sit for >10 mins.
    • Optional: Add fresh 10% bleach solution to glassware.
  4. Pour solution down the drain.
  5. Rinse thoroughly 5X with tap water and 5X with DI water.
    • Tip: If you’re washing test tubes, you can sandwich the test tubes between two racks to make rinsing easier.
  6. If you’re washing test tubes caps, they do not need to be bleached. If they’ve come into contact with bacterial culture, do not soak the caps in bleach. This will cause them to degrade. Simply rinse thoroughly with tap water and DI water.
    • Tip: You can fill a large receptacle with the caps and rinse all the caps at the same time.
  7. If you notice rings or residue after the glassware has dried, proceed to either the “Cleaning with Chromerge” or “Cleaning with Nitric Acid” protocols.

For glassware used for media:

  1. Wash glassware at the sink labeled “Media Wash Station.”
  2. Rinse thoroughly 5X with tap water and 5X with DI water.
  3. If you notice rings or residue after the glassware has dried, proceed to either the “Cleaning with Chromerge” or “Cleaning with Nitric Acid” protocols

Cleaning with Nitric Acid

Notes:

  • Use in the hood. ALWAYS wear a lab coat, gloves, and goggles.
  • Nitric acid can be found in the “Acids Cabinet” located under Fume Hood 1.

Disposal:

  • Do not pour concentrated nitric acid down the drain! Thoroughly dilute the spent acid in a beaker already containing water in the fume hood. Pour the diluted acid down the drain.

Procedure:

  • Transfer desired amount directly into DRY and previously rinsed vessel to be cleaned. Tilt to coat sides. If needed, leave in the hood for short while.
  • Dispose of waste nitric acid per the “Disposal” instructions.
  • Rinse glassware 5X with tap water and 5X with DI water. Remember that the addition of water to any significant amount of strong acid will heat up, often to the boiling point, so be careful. Pour slowly, with the flask already in the sink, watch for “heat”. Add enough water that there is plenty of extra to cool down the reaction. Don’t burn your hand on the glass or splash hot liquid onto yourself.
  • If you still notice rings or residue after the glassware has dried, proceed to the “Cleaning with Chromerge” protocol.

Cleaning with Chromerge

From: David Stevenson

Notes:

  • Chromerge should only be used if the “Washing Dishes” and the “Cleaning with Nitric Acid” protocols have failed, and residue remains.
  • Chromerge is known to be carcinogenic. Use in the hood – double glove, vinyl is best. ALWAYS wear a lab coat and goggles. Be aware that due to the strong oxidizing potential, even the tiniest drop will corrode clothing.
  • Chromerge can be found in the “Acids Cabinet” located under Fume Hood 1.
  • Never use Chromerge on metals, and pipette ONLY with glass.
  • Do NOT mix Chromerge with any other cleaning solutions, especially organics and chlorine – this could release HIGHLY toxic vapors. IF any vapors are seen to rise from a vessel being cleaned, step away. If in the sink step away and have everyone leave the room – these could be very toxic.
  • Nitric acid will clean glassware as well and should be considered as a safer alternative to Chromerge.
  • Chromerge is a mixture of concentrated sulfuric (H2SO4) and chromic acid (H2CrO4), itself a hydrated form of chromium oxide. In many ways these are similar compounds. Both are powerful acids and highly oxidizing acids (both are in the +6 oxidation states – note that on the periodic table S is in group 6A and chromium is in group 6B). Both these traits contribute to its efficacy for cleaning applications.
  • Chromerge turns green when spent, mostly due to the lowering of the chromium oxidation state to +3 (and others) – do not use when green and refer to the “Disposal” section.

Solution Preparation:

  • See Dave before preparing Chromerge solution.
  • Concentrated Chromerge solution is located on Dave’s bench.
  • Empty a 25mL bottle of concentrated Chromerge into 4L of sulfuric acid. Store in a bin in the “Acids Cabinet” located under Fume Hood 1 and attach the provided warning label to the receptacle.
  • A solution made this way will not last forever. It may be viable for only about a month.

Disposal:

  • Do not pour Chromerge down the drain! Pour spent solution in the bottle labeled “Waste Chromerge,” located in Fume Hood 1. Spent solution is hazardous and will be picked up by a Chemical Safety Officer both because it is a strong acid, and it contains the dangerous heavy metal chromium (see Dave if waste is full).

Procedure:

  • Transfer desired amount (minimal) directly into DRY and previously rinsed vessel to be cleaned. Tilt to coat sides. If needed, leave in the hood for short while. In most cases glassware will be cleared almost instantly.
  • When clean, if Chromerge remains orange, return to initial bottle – it can be re-used. If green, transfer to the “Waste Chromerge” bottle (kept in Fume Hood 1).
  • At this point glassware can be carefully rinsed (5X with tap water and 5X with DI water). Remember that the addition of water to any significant amount of Chromerge will heat up, often to the boiling point, so be careful. Pour slowly, with the flask already in the sink, watch for “heat”. Add enough water that there is plenty of extra to cool down the reaction. Don’t burn your hand on the glass or splash hot liquid onto yourself.

Running the Wang Lab SpeedVac Centrifuge

Procedure:

  1. Before starting, ensure the vacuum valve is closed.
    1. The valve is located along the tubing on the back of the centrifuge. Closed is perpendicular to the tubing, open is parallel.
  2. Place samples in the centrifuge.
  3. Turn rotor on.
  4. Turn the condensation trap on.
  5. Turn vacuum pump on (underneath the table).
  6. Open the valve to establish vacuum.

Shutdown procedure:

  1. Turn the vacuum pump off (underneath the table).
  2. Turn the condensation trap off.
    1. If you’re not sure if your samples are completely dry, keep the condensation trap on.
  3. Slowly close the valve.
  4. Turn off the rotor.