Tools
Tools
Basler, N., Xenikoudakis, G., Westbury, M.V., Song, L., Sheng, G. and Barlow, A. 
ORCID: 0000-0002-5532-9458,
2017.
Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone.
BMC Research Notes, 10 (1): 754.
ISSN 1756-0500
|
Text
1233243_Barlow.pdf - Published version Download (1MB) | Preview |
Abstract
Objective: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but varying results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).
Results: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine–cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeogenomic studies, providing sufficient material is available.
| Item Type: | Journal article | ||||||
|---|---|---|---|---|---|---|---|
| Publication Title: | BMC Research Notes | ||||||
| Creators: | Basler, N., Xenikoudakis, G., Westbury, M.V., Song, L., Sheng, G. and Barlow, A. | ||||||
| Publisher: | Springer | ||||||
| Date: | 20 December 2017 | ||||||
| Volume: | 10 | ||||||
| Number: | 1 | ||||||
| ISSN: | 1756-0500 | ||||||
| Identifiers: |
|
||||||
| Divisions: | Schools > School of Science and Technology | ||||||
| Record created by: | Jonathan Gallacher | ||||||
| Date Added: | 13 Nov 2019 11:43 | ||||||
| Last Modified: | 13 Nov 2019 11:43 | ||||||
| URI: | https://irep.ntu.ac.uk/id/eprint/38245 |
Actions (login required)
 |
Edit View |
Views
Views per month over past year
Downloads
Downloads per month over past year
