Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

No ancient pathogen DNA in petrous bones

ABSTRACT: Ancient pathogen DNA in human teeth and petrous bones

PROVIDER: PRJEB24937 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2300290.fastq.gz	Fastqsanger.gz
	ERR2300300.fastq.gz	Fastqsanger.gz
	ERR2300310.fastq.gz	Fastqsanger.gz
	ERR2300320.fastq.gz	Fastqsanger.gz
	ERR2300291.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 34

Similar Datasets

Ancient DNA teeth

Project description:The data set contains MS/MS data on teeth extracts for Ancient DNA teeth samples ran in both positive and Negative ionization modes

2018-12-19 | MSV000083264 | MassIVE

Bleach improves ancient DNA recovery from bones

Project description:Combining bleach and mild pre-digestion improves ancient DNA recovery from bones

| PRJEB15516 | ENA

GNPS_Ancient DNA teeth

Project description:The data set contains MS/MS data on teeth extracts for Ancient DNA teeth samples ran in both positive and Negative ionization modes

2018-12-19 | MSV000083264 | GNPS

CT-scan ancient DNA

Project description:Optimized DNA sampling of ancient bones using Computed Tomography (CT) scans

| PRJEB25493 | ENA

Protein Extraction from Ancient Teeth and Dental Calculus Compatible with Subsequent DNA Extraction

Project description:Dental calculus is becoming a crucial material in the study of past populations, with increasing interest in its proteomic and genomic content. Here we suggest further development of protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth. We then applied the optimised protocol to ancient teeth to limit the destruction of calculus, as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archaeological context. Finally, the applicability of the protocol was proven on samples of ancient calculus.

2023-09-11 | PXD042668 | Pride

Transcription profiling of mouse protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae), mandibular bone and teeth to obtain basal gene expression levels

Project description:Pilot study; Analysis of basal gene expression of the protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae) and mandibular bone and teeth Experiment Overall Design: RNA extraction from normal bone

2008-11-22 | E-GEOD-13563 | biostudies-arrayexpress

Minimally Destructive DNA Extraction from Ancient Teeth

Project description:A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

| PRJEB32750 | ENA

Improving DNA extraction from ancient bones

Project description:Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

| PRJEB10532 | ENA

Ancient pathogen DNA in human teeth and petrous bones.

Project description:Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade-off must be considered when designing the sampling strategy for an aDNA project.

| S-EPMC5869295 | biostudies-literature

Successive protein extraction using hydroxylamine to increase the depth of proteome coverage in fresh, forensic and archaeological bones

Project description:Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, in particular, collagen-containing tissues such as bones and teeth. Here we present the application of a chemi-cal digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical and archaeological samples. We are describing and discussing two protocols, one using hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another focusing directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including increasing the sequence coverage and number of peptides detected in modern and archaeological samples, and increasing the number of proteins identified in archaeological samples. Targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights considering both fresh and ancient mineral-ized samples.

2024-03-28 | PXD046969 | 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