Standard DNA Extraction Guidelines

The following guidelines apply to those submitting biological samples for DNA extraction. These guidelines are appropriate for whole blood, animal tissues, animal/bacterial cells, and plant tissues where resulting DNA will be used for short-read applications on Illumina and metagenomic/amplicon applications on Oxford Nanopore and PacBio instruments.

All General Guidelines must be followed in addition to the guidelines specific to the DNA extraction.

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Biological Safety - General Guidelines

  • We are designated a BSL-2 facility. We can only accept samples that require BSL-1 or BSL-2 containment.
  • Adhere to local and federal regulations when transporting and shipping biological samples.
  • Samples requiring higher than BSL-2 containment or samples delivered to us in an unsafe manner will either be refused or disposed immediately.

Sample Delivery Vessel- General Guidelines

  • The input type and the DNA extraction requested will determine the type of storage vessel. Please see the sample-specific guidelines.

Sample Naming Conventions- General Guidelines

  • Sample names must be de-identified. Samples with Protected Health Information won’t be accepted.
  • Each sample must be identified with a simple, unique identifier. If names have been used in previous submissions, don’t repeat in subsequent submissions.
  • The following conventions are strictly enforced:
    • 3-20 characters
    • A-Z, a-z, 0-9, dash (-) are the ONLY acceptable characters
    • Space, underscore, punctuation, and special characters are NOT ALLOWED
    • No replication

Sample Labeling Conventions- General Guidelines

  • All tubes, plates, and boxes must include the following information.
    • PI name
    • Date
    • Sample name (tubes only)

Shipping or Delivering- General Guidelines

  • A manifest/service request must accompany all shipments or deliveries.
    • Schedule a time for drop off with a staff member at nextgen-seq@biotech.wisc.edu
    • Ship on dry or wet ice to:
      • DNA Sequencing Facility, 425 Henry Mall, 1250 Biotechnology, Madison WI 53706
  • For transport of biological samples on campus, please consult Biological Materials Transport on UW Campus Guidance. For shipment of biological materials, consult local and federal guidelines for safe packaging.
  • Samples delivered to us in an unsafe manner will either be refused or disposed immediately.

Plant Tissues Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. ≤50 mg fresh or lyophilized tissue (1cm2 cutting/punch). Providing >50 mg tissue results in low quality, low yield DNA.
  3. Submitted in capped racks of Qiagen Collection Microtubes (cat # 19560 and 19566) ONLY – UWBC can supply.

See our FAQs on Plant DNA Extraction!

Whole Blood Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. 200 µl (exactly 200 µl used for extraction – can provide up to 5 ml)
  3. Anti-coagulated (EDTA – lavender top, Sodiume Citrate – light blue top, Acid Citrate dDextrose (ACD) – yellow top).
  4. Submitted in shatter-proof collection vessel (BD Vacutainer), 1.5-2 ml cryovial with external threads, or 1.5-2 ml snap-cap tube with tight-fitting lid.

Animal Tissues Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. Up to 20 mg total tissue weight.
  3. Submitted in capped racks of Qiagen Collection Microtubes (cat # 19560 and 19566) ONLY – UWBC can supply. Inquire for low throughput (<24 samples).

Animal Cells Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. Up to 5E6 cultured mammalian cells with media removed (includes culture medium, cryopreservation medium, and PBS).
  3. Submitted in capped racks of Qiagen Collection Microtubes (cat # 19560 and 19566) ONLY – UWBC can supply. Inquire for low throughput (<24 samples).

Bacterial Cells Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. Up to 2E9 cultured bacterial cells with media removed (includes culture medium, cyropersvation medium, and PBS). Growing to mid-log phase (e.g. OD600 of 0.5-0.6 for E. coli) is highly preferred.
  3. Submitted in capped racks of Qiagen Collection Microtubes (cat # 19560 and 19566) ONLY – UWBC can supply. Inquire for low throughput (<24 samples).

Feces or Soil Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. For collection in devices with preservation solutions:
    • Can use collection devices from DNA Genotek (OMD-200) and Zymo (DNA/RNA Shield). Follow manufacturer’s recommendations for processing and storage.
    • Can be submitted in collection device or as 250 µl aliquot in Qiagen PowerBead Pro Tube (cat # 19301) – UWBC can supply.
  3. For unpreserved aliquot of collected samples:
    • Submitted in Qiagen PowerBead Pro Tube (cat # 19301) – UWBC can supply – or in 1.5-2 ml cryovial with external threads, or 1.5-2 ml snap-cap tube with tight-fitting lid.
    • Sample must be provided as a pre-weighed aliquot of up to 250 mg. 100-200 mg is ideal for high quality DNA, while >250mg may cause quality issues.

Environmental Sample Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. Must discuss with UWBC prior to submission.
  3. Collection of matrix/substrate as is or collected on flocked swabs, filter, or other medium.
    • Can use collection devices from DNA Genotek (OMD-200) and Zymo (DNA/RNA Shield). Follow manufacturer’s recommendations for processing and storage.
    • Can be submitted in collection device or as 250 µl aliquot in Qiagen PowerBead Pro Tube (cat # 19301) – UWBC can supply.
    • If unpreserved, must be in Qiagen PowerBead Pro Tube (cat # 19301) – UWBC can supply.
    • Up to 250 mg of matrix/substrate. The mass, volume or dimensions depend on the medium – UWBC will provide guidance.

Preserved Saliva or Buccal Cells Standard DNA Extraction - Specific Guidelines

  1. Follow ALL General Guidelines above.
  2. Only saliva in collection kits from DNA Genotek (OGR-600, OGR-675) and Zymo (SafeCollect) will be accepted. Discuss with UWBC if other. Follow manufacturer’s recommendations for processing and storage.
  3. Can be submitted in collection tube, 1.5-2 ml cryovial with external threads, or 1.5-2 ml snap-cap tube with tight-fitting lid 500 µl to 2 ml.