Quantitative Metagenomics Benchmarking Experiment Data Set

To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%) and deeply sequenced them on the Illumina platform. This dataset summarizes the experimental conditions and results of the detection frequencies of those oligonucleotides as well as detailed descriptions of the DNA reference standards used.

This dataset is associated with the following publication: Davis, B., P. Vikesland, and A. Pruden. Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 59(12): 6192-6202, (2025).

Data and Resources

Field Value
accessLevel public
bureauCode {020:00}
catalog_conformsTo https://project-open-data.cio.gov/v1.1/schema
identifier https://doi.org/10.23719/1532315
license https://pasteur.epa.gov/license/sciencehub-license.html
modified 2024-07-16
programCode {020:000}
publisher U.S. EPA Office of Research and Development (ORD)
publisher_hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
references {https://doi.org/10.1021/acs.est.4c08284,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966778}
resource-type Dataset
source_datajson_identifier true
source_hash 04c4341fd3559066a8e261bd5e806ff4904342959ee5dd70ac32ff7cc949702c
source_schema_version 1.1
Groups
  • AmeriGEOSS
  • National Provider
  • North America
Tags
  • AmeriGEO
  • AmeriGEOSS
  • CKAN
  • GEO
  • GEOSS
  • National
  • North America
  • United States
  • antimicrobial-resistance-amr
  • ddpcr
  • metagenomics
  • qpcr
  • quantitative-accuracy
isopen False
license_id other-license-specified
license_title other-license-specified
maintainer Benjamin Davis
maintainer_email davis.benjamin@epa.gov
metadata_created 2025-09-24T06:34:58.494915
metadata_modified 2025-09-24T06:34:58.494926
notes To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%) and deeply sequenced them on the Illumina platform. This dataset summarizes the experimental conditions and results of the detection frequencies of those oligonucleotides as well as detailed descriptions of the DNA reference standards used. This dataset is associated with the following publication: Davis, B., P. Vikesland, and A. Pruden. Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 59(12): 6192-6202, (2025).
num_resources 2
num_tags 13
title Quantitative Metagenomics Benchmarking Experiment Data Set