PXD015817

PXD015817 is an original dataset announced via ProteomeXchange.

Title	A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus
Description	Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several lines of evidence, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from archaeological dental calculus. We evaluate the protocol on dental calculus from a range of ages and estimated preservation states, and compare it against standard DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaffected by the unified protocol, although minor shifts in the recovered proteome can be detected. Protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas DNA recovery is significantly lowered through the unified protocol. However, DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of evidence from archaeological dental calculus without compromising downstream analyses, thereby minimizing the need for destructive analysis of this finite resource.
HostingRepository	PRIDE
AnnounceDate	2020-04-27
AnnouncementXML	Submission_2020-04-26_23:37:46.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015817
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Zandra Fagernäs
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Deamidated; Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-14 07:13:27	ID requested
⏵ 1	2020-04-26 23:37:47	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: ancient DNA

palaeoproteomics

oral microbiome

dental plaque

metagenomics

Christina Warinner
contact affiliation	Max Planck Institute for the Science of Human History, Department of Archaeogenetics
contact email	warinner@shh.mpg.de
lab head
Zandra Fagernäs
contact affiliation	Max Planck Institute for the Science of Human History
contact email	fagernaes@shh.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015817
     1. Label: PRIDE project
     2. Name: A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus