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Finkelstein Lab Wiki

Freezer Storage & Databases

We maintain databases in the lab’s Google Drive (migrated from the legacy FileMaker Pro database) for organizing our freezer contents. Follow the guidelines below when adding or looking up plasmids, strains, oligos, and -80°C freezer boxes.

Contents

Section titled “Contents”
  1. Plasmid Database
  2. Strain Database
  3. Oligo Database
  4. Racks Database (-80°C Freezer)

1. Plasmid Database

Section titled “1. Plasmid Database”

Store plasmids in a 1.7 mL centrifuge tube by assigning them the next available pIF# in the Google Drive database, printing a label, and storing them in the appropriate -20°C box. Include the concentration of the plasmid on the side of the tube for ease of access.

When adding a plasmid to the database, record:

  1. pIF number: Next sequential number (e.g., if the last plasmid entered was pIF20, yours is pIF21).
  2. Description:
    • Name of the gene
    • Original vector backbone
    • Primers used to construct the plasmid
    • Orientation of the gene of interest
  3. Strain number: Corresponding IF# glycerol stock (see below).
  4. Initials and date.
  5. Resistance markers.
  6. Sequence map uploaded to the database folder.

2. Strain Database

Section titled “2. Strain Database”

To freeze E. coli strains for long-term -80°C storage:

  1. In a 2 mL cryotube, mix either:
    • 1 mL saturated overnight culture with 1 mL sterile 50% glycerol (25% final), or
    • 5 volumes of overnight/exponentially growing culture with 1 volume sterile 80% glycerol (~13% final).
  2. Flash-freeze in liquid nitrogen and store in the appropriate -80°C rack. Strains stored this way remain viable for >25 years.

When adding a strain to the Google Drive database, record:

  1. IF number: Next sequential IF#.
  2. Strain background (e.g., DH5α, DH10Bac, Rosetta(DE3)pLysS, ArcticExpress).
  3. Plasmid carried (pIF# and gene of interest).
  4. Resistance marker.
  5. Initials and date.

3. Oligo Database

Section titled “3. Oligo Database”

Oligos are stored at 100 µM upon receipt in the IDT tube they arrived in. Resuspend the dried oligo in ddH2O (or TE), assign it the next number in the Google Drive database, print a label, and store it in the appropriate box in the -20°C freezer.

4. Racks Database (-80°C Freezer)

Section titled “4. Racks Database (-80°C Freezer)”

When a protein is purified or received externally, or when you add new cell pellets or boxes of any kind, aliquot and store them in a labeled box in the -80°C freezer:

  • Each -80°C freezer is designated by a double letter (AA, BB, CC, etc.).
  • Each rack is numbered (1, 2, etc.).
  • Each rack has 5 rows (1–5) and 4 box depth positions (a–d). For example, the third row of the second rack in the front-most box position is labeled 2.3a.

When adding or removing a box, update the Racks Database in Google Drive with:

  1. Freezer and rack location (e.g., AA 2.3a)
  2. Date made
  3. Description of contents
  4. Your initials (when a box is emptied, remove the physical box and clear its slot in the database)