Guidelines For Genetics Protocol Development Combined
Guidelines For Genetics Protocol Development Combined
DNA extraction is required for many molecular biology applications, and many commercial kits
are available to isolate DNA from a variety of source materials. The quality and purity of the
extracted DNA should be suitable for the intended downstream analyses. These days, most labs
use commercial DNA extraction kits (rather than the traditional phenol-chloroform method),
which employ spin columns, for DNA isolation. Spin columns contain a silica resin that
selectively binds DNA, depending on the salt conditions and other factors influenced by
the extraction method. These kits are generally much easier and faster to use than traditional
methods, and do not require significant expertise. However, regardless of the kit used, and/or if
the lab must optimize a protocol based on available supplies and reagents, it is important to
understand the basic criteria that any method of DNA isolation must meet to determine whether a
protocol is a suitable alternative, particularly for fecal DNA because of the low quantity and
quality of the DNA.
For any sample type, a kit or protocol should satisfy the following criteria: 1. efficient
extraction of DNA, 2. successful removal of contaminants, 3. production of sufficient amount of
DNA for downstream workflow, and 4. isolation of high quality and high purity DNA. The
following is a review of each basic step involved in all DNA extraction methods, and guidelines
for selecting protocols and reagents to ensure the above criteria are met.
Purification of archive-quality DNA from fecal cells in suspension using the Gentra®
Puregene® Tissue Kit
Equipment and reagents
Phosphate-buffered saline (PBS) = 50 mM potassium phosphate, 150 mM NaCl; pH 7.2
Cell lysis solution (0.5% SDS, 8% PVP-10, 250 mM NaCl, 25 mM Na-DETA, 200 mM Tris-
HCl pH7.5)
Elution buffer-10 mM Tris-Cl, 0.5 mM EDTA; pH 9.0.
Protein precipitation solution
100% isopropanol
70% ethanol (do not use denatured alcohol)
Pipets and pipet tips
1.5 mL microcentrifuge tubes
Microentrifuge
Water bath or heat block
Crushed ice
Absorbent paper/kimwipes™
Recommended: glycogen solution 20mg/mL
Optional: RNase A solution
Procedure:
1. Dilute 1–2 g stool in 10 ml PBS, and let the debris settle.
2. After the debris has settled, transfer 100 μl of the supernatant to a clean 1.5 ml
microcentrifuge tube.
3. Add 500 μl Cell Lysis Solution to 100 μl fecal cells in PBS, and mix by pipetting up and
down.
Note: If the sample has a high protein content, 550 μl Cell Lysis Solution may be added
to 50 μl sample.
4. Add 3 μl Proteinase K (20 mg/ml) and incubate lysate at 55°C for 1 h to overnight.
If you wish to include an optional RNase treatment, go to step 4a, otherwise proceed
with step 5.
4a. Add 3 μl RNase A Solution to the cell lysate, and mix by inverting the tube 25 times.
5. Quickly cool the sample to room temperature (15–25°C) by placing on ice for 1 min.
6. Add 200 μl Protein Precipitation Solution to the cell lysate, and vortex vigorously for 20s
at high speed.
7. Incubate on ice for 5 min.
8. Centrifuge at 13,000–16,000 x g for 3 min. The precipitated proteins should form a tight
pellet. Repeat if pellet not well-formed.
9. Pipet 600 μl isopropanol into a clean 1.5 ml microcentrifuge tube.
10. Recommended: Add 1 μl Glycogen Solution (20 mg/ml).
11. Add the supernatant from step 9 by pouring carefully. Make sure not to dislodge the
protein pellet when transferring the supernatant.
12. Mix by inverting gently 50 times and incubate at room temperature for 5 min.
13. Centrifuge at 13,000–16,000 x g for 5 min. The DNA may be visible as a small white
pellet, depending on yield.
14. Carefully discard the supernatant. Drain the tube on a clean piece of absorbent paper,
taking care that the pellet remains in the tube.
15. Add 600 μl of 70% ethanol, and invert gently several times to wash the DNA pellet.
16. Centrifuge at 13,000–16,000 x g for 1 min.
17. Carefully discard the supernatant. Drain the tube on a clean piece of absorbent paper,
taking care that the pellet remains in the tube. The pellet might be loose and easily
dislodged.
18. Allow DNA to air dry at room temperature for 10–15 min. Make sure tube is dry before
proceeding.
19. Add 20 μl DNA Hydration Solution. 100-200 μl of elution buffer is recommended to
ensure enough sample is available for downstream analyses. Low yields can be increased
by concentrating the sample.
20. Incubate at 65°C for 1 h to dissolve the DNA.
21. Incubate at room temperature overnight with gentle shaking. Ensure tube cap is tightly
closed to avoid leakage. Samples can then be centrifuged briefly and transferred to a storage
tube.
Scat Collection for Host/Prey DNA Protocol
Prepared by: Charlotte Hacker, Duquesne University; Imogene Cancellare, University of Delaware,
Panthera; Dr. Byron Weckworth , Panthera; and Dr. Jan Janecka, Duquesne University
Old – no moisture, discolored (faded or bright white), outside casing may be missing.
Sign, Age, Signs of carnivore presence near the sample, how old the signs appear, and their
Proximity distance to the sample. Examples include scrape, urine, latrines, claw rake,
pugmark, and scent spray.
Feature A geographic feature for the landscape where the scat was found. Examples include
ridgelines, saddles, river drainage bottoms, flat grasslands, and rocky outcrops.
GPS and The GPS coordinates of where the scat was collected in decimal degrees and its
Elevation elevation in meters.
Notes Any additional information that may be useful.
Collection –
● It is imperative that bare hands do not touch the scat. This could lead to contamination
of the next scat sample with the previous one. A new tool for collection should be used
for every scat sample. Latex gloves are ideal, but rocks and sticks can also be used if
gloves are unavailable.
● Using sterile tweezers, fresh gloves, or rocks and sticks, break off/cut a full-cross-section
of the scat. Chunks of scat (full circumference and diameter) that appear freshest/less
dry are best as the DNA is less likely to be degraded and are more useful for diet
analysis. Place the scat into the tube.
Scat being broken apart and Scat being broken apart and Scat being broken apart and
collected with gloves. collected with a rock. collected with tweezers.
● Do not stuff the scat tightly into the tube. Make sure
there remains airspace between the scat and the lid of
the tube. This is so the desiccant can properly dry out
the scat to preserve the DNA inside the scat.
● Remove gloves or set down tools used to handle the
scat.
o Dispose of gloves properly by putting them in a
receptacle bag and then putting that bag in the
appropriate bin after the sampling session
Sample put into tube with airspace
(label and store separately from clean gloves). to ensure it dries properly.
● Place the cap back on the tube securely.
● If using tweezers, sterilize between samples with fire by using a lighter to burn off any
scat or hair on the tweezer for at least 5 seconds (let
cool before packing up tools). Do not touch the end of
the tweezers (the part used to collect the scat) at any
time with your bare hands.
● Place the tube in the collection bag.
● Avoid collecting the entire scat if not necessary in order
to maintain the chemical and visual cues scat provides
within a habitat. Sample marked with nail polish to
avoid recollection in future
● If sampling the same transect repeatedly, mark the sampling efforts.
remainder of the scat with nail polish so that it is not
collected during the next sampling session.
Data Entry –
● Entering data from field sheets into an electronic format relatively soon after sampling
sessions is helpful for organizing samples and preparing them for transport.
● At the end of every field day, take a photo of the datasheet for temporary backup in
case the datasheet is lost or destroyed. This covers the lag time between field collection
and entering the data electronically.
● Open up an excel spreadsheet and enter in the information on your sampling sheets as
written. Save file.
o Note: the names labeled on the collection cups in the field are helpful for
discerning date and collector, but are not practical for lab work later on when
sample names must be written repeatedly on the small surfaces of
microcentrifuge tubes. It is helpful to add an associated lab name to the
collection tubes with the samples.
▪ Line up your cups on a flat surface in order of date, collector, and then
collection number.
▪ Relabel each tube in order with a short prefix related to the sample site
followed by a number. Write this name on both the side of the tube and
its cap. Continue onward for the entire sampling session, picking up each
numeric value from where you left off prior.
▪ Add a “Lab Name” column into your Excel spreadsheet and enter in the
name of each sample corresponding with its field name.
▪ Example:
Field Name Lab Name
2020-06-01-CH-01 DUL01
2020-06-01-CH-02 DUL02
2020-06-01-IC-01 DUL03
2020-06-01-IC-02 DUL04
2020-06-01-IC-03 DUL05
2020-06-02-CH-01 DUL06
2020-06-02-CH-02 DUL07
2020-06-02-CH-03 DUL08
Sample Transport:
● Collected samples should be kept in a cool, dry place after
collection until they can be transported.
● Transport of samples should adhere to local government
and country regulations.
● Place sample tubes in a sealed bag. Label the outside of the
bag with name, material, and number of samples in bag.
● If multiple bags accumulate, place them in a larger box or
sturdy bag. Samples organized, labeled, and
packed for transport.
● All boxes should be reinforced with adequate tape to
ensure samples are secured and arrive safely.
Sample Storage:
● Upon return to the laboratory space, proper sample
storage ensures DNA degradation will not occur.
● Room temperature storage is possible so long as the
ambient temperature is stable.
o Labs that do not have reliable temperature control,
or those which are kept above room temperature
(~20°C), are not adequate for room temperature Samples stored in organized rows
storage at stable room temperature.
o Samples as old as 10 years stored at stable room
temperatures have resulted in successful DNA
extraction when stored in this manner
● Refrigerator or freezer storage should be considered if the
laboratory does not have consistent temperature control.
o Freezing samples halts microbial activity that could
further degrade DNA.
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Created By: Charlotte Hacker, Duquesne University; Imogene Cancellare, University of Delaware, Panthera; Dr. Byron Weckworth, Panthera; Dr. Jan E. Janecka, Duquesne University