Maximizing Efficiency in sedimentary ancient DNA Analysis: A Novel Extract Pooling Approach
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB67982 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
Project description:Metagenomic reconstruction of prokaryotes and eukaryotes using shotgun sequenced sedimentary ancient DNA in Upper Lake Constance
| PRJEB76926 | ENA
Project description:Sedimentary ancient DNA shotgun metagenomics of marine sediment core SO201-2-12KL from teh North Pacific
| PRJEB46821 | ENA
Project description:Ancient metagenomics from a sediment core from Lake Naleng, southeastern Tibetan Plateau
| PRJEB74036 | ENA
Project description:DE microRNAs between normal bone and ancient osteosarcoma
2019-06-21 | GSE118540 | GEO
Project description:Environmental dynamics from sedimentary ancient DNA in river and archaeological deposits of the Carpathian Basin
| PRJEB81156 | ENA
Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerably extend be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism.
2012-12-31 | GSE30594 | GEO
Project description:This dataset include the raw sedimentary ancient DNA metabarcoding sequencing data in "Holocene rangeland characteristics on the northeastern Tibetan Plateau in relation to climate and pastoralism from sedimentary ancient DNA"
| PRJEB77355 | ENA
Project description:The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Microarray analysis revealed several classes of significantly regulated genes which could to a considerably extend be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism. Microarray analysis were performed with early life stages of zebrafish exposed to 2 sediment extracts from the Upper part of the River Rhine, Germany. The expression profile as then compared to the expression pattern of model toxicants, such as, 4-chloroaniline, Cadmium, DDT, TCDD, and Valproic acid (Gene Expression Omnibus Series GSE9357). Additionally, combining mechanism-specific bioassays as well as chemical analysis of the sediments to the gene expression data has contributed to a more comprehensive view on the hazard potential of the sediments.
2012-12-31 | E-GEOD-30594 | biostudies-arrayexpress