Difference between revisions of "Sample Collection"
(→Safety, Ethics, and Legality) |
(→Safety, Ethics, and Legality) |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | =Amount= | + | =General Considerations= |
| + | |||
| + | ==Amount== | ||
There is a lot of DNA, especially mitochondrial DNA, in living multi-cellular tissue. DNA is also a fairly stable molecule at normal to low temperatures and if functional nuclease enzymes are not around. If a sample is fresh and unprocessed and you are amplifying DNA by PCR think small. Only a tiny sample, on the order of cubic millimeters, is necessary to result in good DNA sequencing results. A common mistake made by new students is to try to extact DNA from too much tissue sample, the excess proteins, lipids, and carbohydrates can overwhelm and clog up the materials used to purify the DNA. | There is a lot of DNA, especially mitochondrial DNA, in living multi-cellular tissue. DNA is also a fairly stable molecule at normal to low temperatures and if functional nuclease enzymes are not around. If a sample is fresh and unprocessed and you are amplifying DNA by PCR think small. Only a tiny sample, on the order of cubic millimeters, is necessary to result in good DNA sequencing results. A common mistake made by new students is to try to extact DNA from too much tissue sample, the excess proteins, lipids, and carbohydrates can overwhelm and clog up the materials used to purify the DNA. | ||
| − | =Conditions= | + | ==Conditions== |
Avoid samples that have been exposed to high temperatures, are old, or highly processed. A fresh raw porkchop contains lots of DNA but a can of SPAM contains almost no DNA. Also consider the tissue type. Pulpy fruit interiors contain a lot of sugars while the leaf of the same plant may contain much more DNA per unit volume or weight. Bacterial or fungal growth on a sample will also quickly destroy DNA and contaminate it with their own DNA. Samples that are kept dry or continuously frozen can contain recoverable amounts of DNA for decades up to thousands of years. Hot, wet, old conditions are bad. Cold, dry, young conditions are good. | Avoid samples that have been exposed to high temperatures, are old, or highly processed. A fresh raw porkchop contains lots of DNA but a can of SPAM contains almost no DNA. Also consider the tissue type. Pulpy fruit interiors contain a lot of sugars while the leaf of the same plant may contain much more DNA per unit volume or weight. Bacterial or fungal growth on a sample will also quickly destroy DNA and contaminate it with their own DNA. Samples that are kept dry or continuously frozen can contain recoverable amounts of DNA for decades up to thousands of years. Hot, wet, old conditions are bad. Cold, dry, young conditions are good. | ||
| − | =Safety, Ethics, and Legality= | + | ==Safety, Ethics, and Legality== |
| − | Even more important considerations are the safety, ethics, and legality of obtaining a sample. Do not put yourself at risk by collecting road kill or samples off of cliffs, for example, if there is an element of danger to the situation. Do not expose yourself to potential diseases or parasites from a raw untreated tissue sample. Wear appropriate [[PPE]] such as gloves when dissecting. Also note that there are nucleases on the surface of human skin ([https://www.sciencedirect.com/science/article/pii/S0022202X15474020]). Do not trespass or take organisms from no-take-fishing-zones, for example. Do not collect samples from other people (human subjects require [[IRB]] approval). Your own DNA, say from a cheek swab, is okay for work that you are doing yourself, but this is quickly approaching a gray zone. Do not interact with live vertebrates in any way for the purposes of DNA sample collection (research with vertebrates requires [[IACUC]] approval). However, any non-living vertebrate sample that is acquired commercially, such as from a grocery store, is fair game. A fin clipping from a fish a relative legally caught for traditional fishing purposes, not for obtaining a DNA sample for research, is okay but this is also quickly approaching a gray zone. In general plants, fungi, invertebrates, and commercial (raw, fresh) food are okay to collect. However, do not harm a specially protected species such as threatened or endangered species, coral, [[CITES]] listed species, or anything that is illegal for you to posses. If | + | Even more important considerations are the safety, ethics, and legality of obtaining a sample. Do not put yourself at risk by collecting road kill or samples off of cliffs, for example, if there is an element of danger to the situation. Do not expose yourself to potential diseases or parasites from a raw untreated tissue sample. Wear appropriate [[PPE]] such as gloves when dissecting. Also note that there are nucleases on the surface of human skin that can break down DNA and especially RNA ([https://www.sciencedirect.com/science/article/pii/S0022202X15474020]). Do not trespass or take organisms from no-take-fishing-zones, for example. Do not collect samples from other people (human subjects require [[IRB]] approval). Your own DNA, say from a cheek swab, is okay for work that you are doing yourself, but this is quickly approaching a gray zone. Do not interact with live vertebrates in any way for the purposes of DNA sample collection (research with vertebrates requires [[IACUC]] approval). However, any non-living vertebrate sample that is acquired commercially, such as from a grocery store, is fair game. A fin clipping from a fish a relative legally caught for traditional fishing purposes, not for obtaining a DNA sample for research, is okay but this is also quickly approaching a gray zone. In general plants, fungi, invertebrates, and commercial (raw, fresh) food are okay to collect. However, do not harm a specially protected species such as threatened or endangered species, coral, [[CITES]] listed species, or anything that is illegal for you to posses. If [[Permits]] are required make sure you have them. |
| − | =Tissue Sample Storage= | + | ==Tissue Sample Storage== |
Samples are ideally stored frozen or in ethanol, the higher the percentage the better, 70% or above. If you have it acidic [[ASE]] (Ammonium sulfate, Sodium citrate, [[EDTA]]) preservative or equivalent is also a great DNA preservative for periods of time at room temperature. | Samples are ideally stored frozen or in ethanol, the higher the percentage the better, 70% or above. If you have it acidic [[ASE]] (Ammonium sulfate, Sodium citrate, [[EDTA]]) preservative or equivalent is also a great DNA preservative for periods of time at room temperature. | ||
| + | |||
| + | =What Links Here= | ||
| + | {{Special:WhatLinksHere/{{FULLPAGENAME}}}} | ||
Latest revision as of 20:22, 1 August 2018
Contents
General Considerations
Amount
There is a lot of DNA, especially mitochondrial DNA, in living multi-cellular tissue. DNA is also a fairly stable molecule at normal to low temperatures and if functional nuclease enzymes are not around. If a sample is fresh and unprocessed and you are amplifying DNA by PCR think small. Only a tiny sample, on the order of cubic millimeters, is necessary to result in good DNA sequencing results. A common mistake made by new students is to try to extact DNA from too much tissue sample, the excess proteins, lipids, and carbohydrates can overwhelm and clog up the materials used to purify the DNA.
Conditions
Avoid samples that have been exposed to high temperatures, are old, or highly processed. A fresh raw porkchop contains lots of DNA but a can of SPAM contains almost no DNA. Also consider the tissue type. Pulpy fruit interiors contain a lot of sugars while the leaf of the same plant may contain much more DNA per unit volume or weight. Bacterial or fungal growth on a sample will also quickly destroy DNA and contaminate it with their own DNA. Samples that are kept dry or continuously frozen can contain recoverable amounts of DNA for decades up to thousands of years. Hot, wet, old conditions are bad. Cold, dry, young conditions are good.
Safety, Ethics, and Legality
Even more important considerations are the safety, ethics, and legality of obtaining a sample. Do not put yourself at risk by collecting road kill or samples off of cliffs, for example, if there is an element of danger to the situation. Do not expose yourself to potential diseases or parasites from a raw untreated tissue sample. Wear appropriate PPE such as gloves when dissecting. Also note that there are nucleases on the surface of human skin that can break down DNA and especially RNA ([1]). Do not trespass or take organisms from no-take-fishing-zones, for example. Do not collect samples from other people (human subjects require IRB approval). Your own DNA, say from a cheek swab, is okay for work that you are doing yourself, but this is quickly approaching a gray zone. Do not interact with live vertebrates in any way for the purposes of DNA sample collection (research with vertebrates requires IACUC approval). However, any non-living vertebrate sample that is acquired commercially, such as from a grocery store, is fair game. A fin clipping from a fish a relative legally caught for traditional fishing purposes, not for obtaining a DNA sample for research, is okay but this is also quickly approaching a gray zone. In general plants, fungi, invertebrates, and commercial (raw, fresh) food are okay to collect. However, do not harm a specially protected species such as threatened or endangered species, coral, CITES listed species, or anything that is illegal for you to posses. If Permits are required make sure you have them.
Tissue Sample Storage
Samples are ideally stored frozen or in ethanol, the higher the percentage the better, 70% or above. If you have it acidic ASE (Ammonium sulfate, Sodium citrate, EDTA) preservative or equivalent is also a great DNA preservative for periods of time at room temperature.
