데이터셋 상세
미국
Diatom DNA sequence data
The raw data consisted of demultiplexed fastq files pairs (R1.fastq and R2.fastq) per sample accessible on the NCBI Sequences Read Archive (SRA) under the BioProject accession numbers PRJNA1187555 for experiments E1 and E3 and PRJNA1187576 for E2 and E4. This dataset is associated with the following publication: Valentin, V., S. Rivera, E. Acs, S. Almeida, K. Andree, L. Apothéloz-Perret-Gentil, B. Bailet, A. Baričević, K. Beentjes, J. Bettig, A. Bouchez, C. Camilla, C. Chardon, M. Duleba, T. Elersek, C. Genthon, M. Jablonska, L. Jacas, M. Kahlert, M. Kelly, J. Macher, F. Mauri, M. Moletta-Denat, A. Mortágua, J. Pawlowski, J. Pérez-Burillo, M. Pfannkuchen, E. Pilgrim, P. Panayiota, F. Rimet, K. Stanic, K. Tapolczai, S. Theroux, R. Trobajo, B. Van der Hoorn, M. Vasquez, M. Vidal, D. Wanless, J. Warren, J. Zimmermann, and B. Paix. Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring. Metabarcoding and Metagenomics. Pensoft Publishers, Sofia, BULGARIA, e133264, (2025).
데이터 정보
연관 데이터
Metadata for Carlisle et al. A Web-Based Tool for Assessing the Condition of Benthic Diatom Assemblages in Streams and Rivers of the Conterminous United States
공공데이터포털
R code and data files used to identify diatom metrics that are robust to taxonomic inconsistency. The R code run a goodness of fit analysis to determine how much variation is explained by analyst in a diatom dataset that has been harmonized for taxonomic consistency compared to the original raw dataset. This dataset is associated with the following publication: Carlisle, D., S. Spaulding, M. Tyree, N. Schulte, S. Lee, R. Mitchell, and A. Pollard. A web-based tool for assessing the condition of benthic diatom assemblages in streams and rivers of the conterminous United States manuscript. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 135: 1-13, (2022).
EPAdata MLS paper1
공공데이터포털
EPA Draft Method C QPCR cycle threshold (Ct) measurements of standardized reference materials as described in D-EMMD-MEB-025-QAPP-01 and Journal article. This dataset is associated with the following publication: Sivaganesan, M., T. Aw, S. Briggs, E. Dreelin, A. Aslan, S. Dorevitch, A. Shrestha, N. Isaacs, J. Kinzelman, G. Kleinheinz, R. Noble, R. Rediske, B. Scull, S. Rosenberg, B. Weberman, T. Sivy, B. Southwell, S. Siefring, K. Oshima, and R. Haugland. Standardized data quality acceptance criteria for a rapid Escherichia coli qPCR method (Draft Method C) for water quality monitoring at recreational beaches. WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 156: 456-464, (2019).
EPAdata MLS paper2
공공데이터포털
EPA Draft Method C QPCR cycle threshold (Ct) measurements of standardized reference materials and blinded test samples as described in D-EMMD-MEB-025-QAPP-01 and Journal article. This dataset is associated with the following publication: Aw, T., M. Sivaganesan, S. Briggs, E. Dreelin, A. Aslan, S. Dorevitch, A. Shrestha, N. Isaacs, J. Kinzelman, G. Kleinheinz, R. Noble, R. Rediske, B. Scull, S. Rosenberg, B. Weberman, T. Sivy, B. Southwell, S. Siefring, K. Oshima, and R. Haugland. Evaluation of multiple laboratory performance and variability in analysis of recreational freshwaters by a rapid Escherichia coli qPCR method (Draft Method C). WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 156: 465-474, (2019).
EPAdata MLS paper2
공공데이터포털
EPA Draft Method C QPCR cycle threshold (Ct) measurements of standardized reference materials and blinded test samples as described in D-EMMD-MEB-025-QAPP-01 and Journal article. This dataset is associated with the following publication: Aw, T., M. Sivaganesan, S. Briggs, E. Dreelin, A. Aslan, S. Dorevitch, A. Shrestha, N. Isaacs, J. Kinzelman, G. Kleinheinz, R. Noble, R. Rediske, B. Scull, S. Rosenberg, B. Weberman, T. Sivy, B. Southwell, S. Siefring, K. Oshima, and R. Haugland. Evaluation of multiple laboratory performance and variability in analysis of recreational freshwaters by a rapid Escherichia coli qPCR method (Draft Method C). WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 156: 465-474, (2019).
Dataset for development and evaluation of a qPCR method modification that mitigates DNA recovery losses for analyses of E. coli fecal indicator bacteria in Great Lakes region recreational waters
공공데이터포털
Results previously reported by EPA/ORD on the modified method have led to its adoption into a Standard Operating Procedure for labs performing qPCR analyses for E. coli at recreational beaches in the state of Michigan. This dataset provides further documentation of the performance and applicability of the modified method for recreational beach water testing including data from an extensive survey that can be used to determine when and where unacceptable levels of DNA losses may occur with and without this method modification in the Great Lakes region. Please see the attached dataset description document for additional information.
EPA data for Lane et al 2020 Water
공공데이터포털
QPCR standard curve data and example test sample data. This dataset is associated with the following publication: Lane, M.J., J.N. McNair, R.R. Rediske, S. Briggs, M. Sivaganesan, and R. Haugland. Simplified Analysis of Measurement Data from A Rapid E. coli qPCR Method (EPA Draft Method C) Using A Standardized Excel Workbook. WATER. MDPI AG, Basel, SWITZERLAND, 12(3): 775, (2020).
Supplementary material for Lee et al. in review: Harmonization and Revision of a National Diatom Dataset for Use in the Development of Water Quality Indicators
공공데이터포털
ABSTRACT Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008-2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variability explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides) species complex, and elevated Nitzschia, Diploneis, and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora, Mayamaea, and Psammodictyon, indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove the analyst signal, this work clarifies the extent of the problem and provides a method to minimize analyst signal. Resolution of these taxonomic issues makes large datasets such as the NRSA more suitable for the development of diatom-based water quality indicators. This dataset is associated with the following publication: Lee, S., I. Bishop, S. Spaulding, R. Mitchell, and L. Yuan. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets.. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 102: 166-174, (2019). NOTE: This dataset has been removed from public access due to revocation. Please refer inquiries regarding this dataset to the listed contact person.
Interlaboratory Performance and Quantitative PCR Performance Benchmarks for NIST SRM® 2917 Monitoring qPCR Assays
공공데이터포털
qPCR assay interlaboratory measurements using NIST SRM 2917. This dataset is associated with the following publication: Sivaganesan, M., J. Willis, M. Karim, A. Babatola, D. Catoe, A.B. Boehm, M. Wilder, H. Green, A. Lobos, V.J. Harwood, S. Hertel, R. Klepikow, M.F. Howard, P. Laksanalamai, A. Roundtree, M. Mattioli, S. Eytcheson, M. Molina, M. Lane, R. Rediske, A. Ronan, N. D'Souza, J.B. Rose, A. Shrestha, C. Hoar, A.I. Silverman, W. Faulkner, K. Wickman, J.G. Kralj, S. Servetas, M.E. Hunter, S.A. Jackson, and O. Shanks. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 225: 119162, (2022).
Metabarcoding of environmental DNA samples collected below Jackson Lake Dam (Wyoming) and Palisades Reservoir (Idaho) in 2021-2022 (ver. 2.0, November 2024)
공공데이터포털
These metadata contain links to the original sequences on GenBank. These data show the final OTU and metadata tables for each environmental sample collected. Additionally, we included OTU tables resulting from bioinformatic decontamination steps (using microDecon) in R.
Environmental DNA qPCR concentration results and environmental covariates from a Montana headwater stream sampled in 2023
공공데이터포털
Environmental DNA quantitative results at the PCR technical replicate level for the target species Arctic Grayling and covariate information associated with these eDNA samples.