Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening Archaeological Bone

ABSTRACT: Screening archaeological bone for palaeogenetic and palaeoproteomic studies

PROVIDER: PRJEB37812 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4029120.fastq.gz	Fastqsanger.gz
	ERR4029130.fastq.gz	Fastqsanger.gz
	ERR4029140.fastq.gz	Fastqsanger.gz
	ERR4029150.fastq.gz	Fastqsanger.gz
	ERR4029160.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 71

Similar Datasets

Poor preservation of antibodies in archaeological human bone and dentine

Project description:The growth of proteomics-based methods in archaeology prompted an investigation of the survival of non-collagenous proteins, specifically immunoglobulin G (IgG), in archaeological human bone and dentine. Over a decade ago reports were published on extracted, immunoreactive archaeological IgG, and the variable yields of IgG molecules detected by Western blots of 1D and 2D SDS-PAGE gels. If IgG can indeed be recovered from archaeological skeletal material, it offers remarkable opportunities for exploring the history of disease - for example in applying functional anti-malarial IgGs to study past patterns of malaria. More recently, the field has seen a move away from immunological approaches and towards the use of shotgun proteomics via mass spectrometry. Using previously published techniques, this study attempted to extract and characterize archaeological IgG proteins. In only one extraction method were immunoglobulin derived peptides identified, and these displayed extensive evidence of degradation. The failure to extract immunoglobulins by all but one method, along with observed patterns of protein degradation, suggests that IgG may be an unsuitable target for detecting disease-associated antigens. This research highlights the importance of revisiting previously ‘successful’ biomolecular methodologies using emerging technologies.

2016-02-08 | PXD002295 | Pride

Archaeological latrine sediment

Project description:Archaeological latrine sediment Raw sequence reads

| PRJNA640385 | ENA

archaeological waterlogged wood

Project description:archaeological waterlogged wood Raw sequence reads

| PRJNA689910 | ENA

Screening archaeological bone for palaeogenetic and palaeoproteomic studies.

Project description:The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.

| S-EPMC7316274 | biostudies-literature

Droulers bone points

Project description:Shotgun sequencing of archaeological bone points from Droulers, Quebec.

| PRJEB23998 | ENA

Low-invasive sampling method for taxonomic for the identification of archaeological and paleontological bone by proteomics of their collagens

Project description:Bone collagen is an important organic material for isotopic measurement, radiocarbon and paleoproteomic analyzes, to provide information on diet, dating, taxonomic identification. Current paleoproteomics methods are destructive and require from a few milligrams to several tenths of milligrams of bone for analysis. In many cultures, bones are raw materials for artefact which are conserved in museum which hampers to damage these precious objects during sampling. Here, we describe a minimal sampling method that identifies collagen, taxonomy and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 5,000 years ago using dermatological skin tape-discs for sampling. The sampled bone micro-powder were digested following our highly optimized eFASP protocol, then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by destructive sampling. Moreover, this sampling method can be performed at archaeological sites or in museums.

2024-07-25 | PXD044039 | Pride

Bone collagen from Pacific salmonid species contains differences allowing for peptide mass fingerprinting for easy identification

Project description:MS/MS spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen.

2019-04-15 | MSV000083687 | MassIVE

Palaeoproteomic variation between cortical and trabecular bone

Project description:Here we provide proteomic datasets of pairs of cortical and trabecular bone from six Early Holocene Caprinae rib fragments from the site of La Draga, Spain, using shotgun proteomics. Our observations on proteome size and protein, peptide, and amino acid degradation have implications for the sampling of archaeological skeletal remains in highly degraded proteomic contexts, where preference should be given to the sampling of cortical bone in order to maximise the retrieval of larger and better-preserved skeletal proteomes.

2024-07-12 | PXD047126 | Pride

Oral Signature Screening Database for Palaeoproteomic Analyses of Dental Calculus

Project description:As the proteomic analysis of dietary peptides retrieved from archaeological materials becomes more common, new methods of authentication need to be considered. Here we present an oral signature screening database (hereafter OSSD) developed specifically for ancient dental calculus. By using the OSSD as a first screening step we hope it can help users quickly identify problematic samples as well as those which could potentially be good candidates for endogenous dietary proteins.

2020-12-04 | MSV000086557 | MassIVE

Comparison of bone demineralization protocols for paleoproteomics applications

Project description:Protocols for bone protein extraction adapted for radiocarbon dating were compared for their capability of being used also for paleoproteomics applications. Eight extraction protocols were tested on modern and archaeological bones. Molecular characterization of the extracts was performed by shot-gun proteomics. The effect of each extraction protocol on species identification through database searchnig was evaluated.

2018-12-11 | PXD010775 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data