Facilities

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Whereas most modern DNA molecules exist as long intact strands, ancient DNA is damaged, enriched in deaminations, and broken into small pieces. The main goal of an ancient DNA facility is to avoid contamination with modern nucleic acids. This is especially true for the analysis of human samples, where the possibility of contamination by the laboratory, museum, archaeological or anthropological coworkers is extremely high. The strict separation of pre-and post- PCR work phases is particularly important to prevent the transfer of modern DNA molecules from the post- to the pre- PCR laboratory. In order to prevent this type of contamination, the two labs are located two floors away from each other.

The main parts of the laboratory:

Ancient DNA clean rooms (pre-PCR laboratory)
The entrance into the ancient DNA clean laboratory leads through three changing rooms where researchers change street clothes and get suited up (bodysuits, gloves, particular shoes, face masks, hairnet). The storage room also houses lab supplies. Every item entering the clean rooms is extensively washed with bleach and subsequently (sodium hypochlorite -NaClO), UV-C irradiated.

No modern DNA work is carried out in the pre-PCR laboratory. Work surfaces, reagents, and equipments are also routinely irradiated and cleaned with bleach to remove any modern DNA. The sample preparation room is partitioned by a specially isolated cabin for the primary cleaning, cutting, and polishing of the samples. It is also equipped with a vacuum sucker. The cleanrooms of the laboratory are under positive air pressure, ensuring a constant pressure gradient through the laboratory with the highest pressure in the DNA extraction room. This room is equipped with a laminar flow box, where the DNA extraction is carried out. The laminar flow box is a special preparatory room is fitted with a fume hood for reagent handling (for dealing with toxic chemicals). We use HPLC-water for reactions and ultrapure water for cleaning purposes.
Post-PCR laboratories
The post-PCR laboratory has two departments. One is composed of a semi-clean room for DNA library handling and a dedicated sequencing room, and the other sector is used for post-PCR analyses. The latter is outfitted with thermocyclers, electrophoresis equipment, and gel documentation systems. PCR's that are set up in the clean rooms are transported to the post-PCR lab where they are amplified and prepared for downstream analyses. The post-PCR laboratory has an extra clean bench, addressed to hybridization capture reactions. This part of the lab is also used for the extraction, amplification, and sequencing of modern DNA samples. To prevent cross-contamination, workflow and sample treatment are strictly pre-PCR -> post-PCR. In the Institute of Archaeogenomics the researchers can process and sequencing of highly degraded DNA samples (see Chapter Methods).