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Data from: DNA sampling between the shells: evaluating non-lethal DNA sampling methods in oysters for high-throughput genotyping

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: August 03, 2026 at 05:01 PM | Dataset Last Updated: July 27, 2026
This dataset includes genotype data for experiments with Pacific and eastern oysters that evaluated genotype concordance between non-lethal DNA samples and lethal tissue samples. Briefly, for each experiment, oysters were relaxed to induce gaping such that the viscera was accessible with a non-lethal swab. Each oyster was swabbed (multiple swab types were tested) then allowed to recover in ambient seawater conditions for a variable period of time. After short-term recovery the oysters were shucked and a lethal adductor tissue sample was taken. The paired samples (one adductor and one swab sample) had DNA extracted and genotype data produced via sequencing array (eastern oyster experiments) or via genotyping-by-sequencing (Pacific oyster experiments). The genotype data was processed and for each paired sample the concordance of genotypes was assessed.

Resources

11 resources available

  • G0124-31-USDA_440-SNPs.map

    MAP
    Download

  • thermofisher-microhaplotypes-raw-data.rds

    RDS
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  • Ion-Code_to_Sample-ID_Key.xlsx

    XLSX
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  • G0922_07_UMD.ped .zip

    ZIP
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  • G0124-31-USDA_QC-TABLE.xlsx

    XLSX
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  • USDA-microhaplotypes-metadata.tsv

    TSV
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  • G0124-31-USDA_440-SNPs.ped

    PED
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  • USDA-microhaplotypes-experiment-metadata.tsv

    TSV
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  • G0124-04-UMD100.ped.zip

    ZIP
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  • G0922-07-UMD_Sample_QC_Table_with BIOPSY sample info.csv

    CSV
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  • USDA-microhaplotypes-raw-sequence-data.tsv

    TSV
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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "005:18"
]
contactPoint 
{
  "fn": "Thompson, Neil, F.",
  "hasEmail": "mailto:neil.thompson@usda.gov"
}
description <p dir="ltr">This dataset includes genotype data for experiments with Pacific and eastern oysters that evaluated genotype concordance between non-lethal DNA samples and lethal tissue samples. Briefly, for each experiment, oysters were relaxed to induce gaping such that the viscera was accessible with a non-lethal swab. Each oyster was swabbed (multiple swab types were tested) then allowed to recover in ambient seawater conditions for a variable period of time. After short-term recovery the oysters were shucked and a lethal adductor tissue sample was taken. The paired samples (one adductor and one swab sample) had DNA extracted and genotype data produced via sequencing array (eastern oyster experiments) or via genotyping-by-sequencing (Pacific oyster experiments). The genotype data was processed and for each paired sample the concordance of genotypes was assessed.</p>
distribution 
[
  {
    "@type": "dcat:Distribution",
    "title": "G0124-31-USDA_440-SNPs.map",
    "format": "map",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/66365894"
  },
  {
    "@type": "dcat:Distribution",
    "title": "thermofisher-microhaplotypes-raw-data.rds",
    "format": "rds",
    "mediaType": "application/gzip",
    "downloadURL": "https://ndownloader.figshare.com/files/66365897"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Ion-Code_to_Sample-ID_Key.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/66365900"
  },
  {
    "@type": "dcat:Distribution",
    "title": "G0922_07_UMD.ped .zip",
    "format": "zip",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/66365903"
  },
  {
    "@type": "dcat:Distribution",
    "title": "G0124-31-USDA_QC-TABLE.xlsx",
    "format": "xlsx",
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://ndownloader.figshare.com/files/66365906"
  },
  {
    "@type": "dcat:Distribution",
    "title": "USDA-microhaplotypes-metadata.tsv",
    "format": "tsv",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/66365909"
  },
  {
    "@type": "dcat:Distribution",
    "title": "G0124-31-USDA_440-SNPs.ped",
    "format": "ped",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/66365912"
  },
  {
    "@type": "dcat:Distribution",
    "title": "USDA-microhaplotypes-experiment-metadata.tsv",
    "format": "tsv",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/66365915"
  },
  {
    "@type": "dcat:Distribution",
    "title": "G0124-04-UMD100.ped.zip",
    "format": "zip",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/66365918"
  },
  {
    "@type": "dcat:Distribution",
    "title": "G0922-07-UMD_Sample_QC_Table_with BIOPSY sample info.csv",
    "format": "csv",
    "mediaType": "text/csv",
    "downloadURL": "https://ndownloader.figshare.com/files/66365921"
  },
  {
    "@type": "dcat:Distribution",
    "title": "USDA-microhaplotypes-raw-sequence-data.tsv",
    "format": "tsv",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/66365924"
  }
]
identifier 10.15482/USDA.ADC/32915762.v1
keyword 
[
  "bivalves",
  "genotype-concordance",
  "genotyping",
  "genotyping-by-sequencing",
  "non-lethal DNA sampling"
]
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2026-07-27
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2026-04-06/2026-04-06
title Data from: DNA sampling between the shells: evaluating non-lethal DNA sampling methods in oysters for high-throughput genotyping

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