Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Maximizing Efficiency in sedimentary ancient DNA Analysis: A Novel Extract Pooling Approach

ABSTRACT: Pooling of ancient sediment samples

PROVIDER: PRJEB67982 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.

Project description:In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.

| S-EPMC11339378 | biostudies-literature

Sedimentary ancient DNA shotgun data Lake Salmon

Project description:Sedimentary ancient DNA shotgun data Lake Salmon sediment core

| PRJEB82717 | ENA

Sedimentary ancient DNA shotgun data Lake Ilirney

Project description:Sedimentary ancient DNA shotgun data Lake Ilirney sediment core

| PRJEB80635 | ENA

Sedimentary ancient DNA shotgun data Lake Bolshoi Toko

Project description:Sedimentary ancient DNA shotgun data Lake Bolshoi Toko sediment core

| PRJEB80642 | ENA

Metaproteomic analyses of microbial community from ancient permafrost

Project description:It remains challenging to study the viability and metabolic activity of microorganisms buried in ancient permafrost. We coupled aspartic acid racemization assay with metaproteomics to constraint the microbial activity of indigenous microbial community entrappped in permafrost sediment over 100 kyr ago.

2021-09-09 | PXD022683 | Pride

Lake Constance sedimentary ancient DNA

Project description:Metagenomic reconstruction of prokaryotes and eukaryotes using shotgun sequenced sedimentary ancient DNA in Upper Lake Constance

| PRJEB76926 | ENA

Sedimentary ancient DNA shotgun data Lake Ulu

Project description:Sedimentary ancient DNA shotgun data Lake Ulu

| PRJEB82635 | ENA

Sedimentary ancient DNA shotgun metagenomics of core SO201-2-12KL

Project description:Sedimentary ancient DNA shotgun metagenomics of marine sediment core SO201-2-12KL from teh North Pacific

| PRJEB46821 | ENA

Sedimentary ancient DNA shotgun data Lake Levinson Lessing

Project description:Sedimentary ancient DNA shotgun data Lake Levinson Lessing

| PRJEB94536 | ENA

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Project description:Ancient metagenomics from a sediment core from Lake Naleng, southeastern Tibetan Plateau