Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Contamination in ancient faunal datasets

ABSTRACT: Low coverage shotgun sequencing of woolly mammoth and ancient canid samples.

PROVIDER: PRJEB41038 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4778300_1.fastq.gz	Fastqsanger.gz
	ERR4778300_2.fastq.gz	Fastqsanger.gz
	ERR4778310_1.fastq.gz	Fastqsanger.gz
	ERR4778310_2.fastq.gz	Fastqsanger.gz
	ERR4778320_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 140

Similar Datasets

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

2024-05-22 | GSE268050 | GEO

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.

Project description:BackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

| S-EPMC7708127 | biostudies-literature

Mammuthus primigenius

Project description:woolly mammoth

| PRJNA16316 | ENA

Project description:Ancient RNA expression profiles from the extinct woolly mammoth

| PRJNA1256124 | ENA

Mammuthus primigenius

Project description:Ancient RNA expression profiles from the extinct woolly mammoth

| PRJNA1190340 | ENA

Project description:Ancient high-coverage shotgun human genomes

| PRJNA670050 | ENA

Proteomics of muscle and bone marrow samples from the 28,000-year-old remains of a woolly mammoth (Mammuthus primigenius).

Project description:The 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. We performed proteomic analyses of muscle and bone marrow samples obtained from the remains to gain information about the repertoire and modifications of proteins.

2019-03-13 | PXD012741 | Pride

Proteomic Analysis of the Shandrin Mammoth by EVA Technology and High-Resolution Mass Spectrometry: What is its Gut Telling Us?

Project description:The investigation about archaeological samples, which are of inestimable value, requires minimally destructive or nondestructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. This paper reports the results of the first-ever analysis of proteins extracted from the EVA film applied to a tissue sample some 40000 years old. In particular, the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), via a shotgun MS-based approach was investigated. Proteomic and peptidomic analysis allowed the exploration of the mammoth dietary plants and its gut bacteria. The results were validated through the level of deamidation and other post-translational modifications of the peptides of the samples, which were used to discrimitate the “original” endogenous peptides from contaminant ones. Overall, the results of the metaproteomic analysis here reported are in accordance with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth.

2021-11-03 | PXD025518 | Pride

Genome reveals low inbreeding in a near-extinction woolly rhinoceros specimen recovered from ancient wolf stomach

Project description:Woolly rhino genome from ancient wolf stomach

| PRJEB77660 | ENA

Arctic ancient eDNA

Project description:Ancient arctic plant and animal eDNA shotgun sequencing dataset

| PRJEB43822 | ENA