Evaluating accuracy of DNA pool construction based on white blood cell counts

Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. This data set was generated to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis.

The dataset includes: 1) pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y). 2) Genotypes or number of copies of B(green) allele (0,1,2). 3) Definitions for each sample.


Resources in this dataset:


  • Resource Title: Pooling Allele Frequencies (paf) for all pools and individual animals.

    File Name: pafAnimal.csv.gz

    Resource Description: Pooling Allele Frequencies (paf) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); paf = X / (X + Y)


  • Resource Title: Genotypes for individuals within pools.

    File Name: g.csv.gz

    Resource Description: Genotypes (number of copies of the B (green) allele (0,1,2)) for individual bovine animals within pools.


  • Resource Title: Sample Definitions .

    File Name: XY Data Key.xlsx

    Resource Description: Definitions for each sample (both pools and individual animals).

Data and Resources

Field Value
accessLevel public
bureauCode {005:18}
catalog_@context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
catalog_conformsTo https://project-open-data.cio.gov/v1.1/schema
catalog_describedBy https://project-open-data.cio.gov/v1.1/schema/catalog.json
identifier 10.15482/USDA.ADC/1520555
license https://www.usa.gov/publicdomain/label/1.0/
modified 2025-05-05
old-spatial {"type": "Point", "coordinates": [-98.159408569336, 40.524858582343]}
programCode {005:040}
publisher Agricultural Research Service
resource-type Dataset
source_datajson_identifier true
source_hash cc4bf756ab88dde86e0d112a6af6e45ec95a301fe5e4a1def1d595f8fef1430f
source_schema_version 1.1
spatial {"type": "Point", "coordinates": [-98.159408569336, 40.524858582343]}
temporal 2020-04-07/2020-04-07
Groups
  • AmeriGEOSS
  • National Provider
  • North America
Tags
  • AmeriGEO
  • AmeriGEOSS
  • CKAN
  • GEO
  • GEOSS
  • National
  • North America
  • United States
  • alleles
  • ars
  • blood
  • blood-volume
  • data-gov
  • gene-frequency
  • genotype
  • genotyping
  • np101
  • sample-pooling
  • spectrophotometers
  • white-blood-cell-count
  • white-blood-cells
isopen False
license_id us-pd
license_title us-pd
maintainer Abrams, Amy
maintainer_email aabrams@berry.edu
metadata_created 2025-09-24T23:21:53.992812
metadata_modified 2025-09-24T23:21:53.992822
notes <p>Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. This data set was generated to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis.</p> <p>The dataset includes: 1) pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y). 2) Genotypes or number of copies of B(green) allele (0,1,2). 3) Definitions for each sample.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Pooling Allele Frequencies (paf) for all pools and individual animals.</p> <p>File Name: pafAnimal.csv.gz</p><p>Resource Description: Pooling Allele Frequencies (paf) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); paf = X / (X + Y)</p></li><br><li><p>Resource Title: Genotypes for individuals within pools.</p> <p>File Name: g.csv.gz</p><p>Resource Description: Genotypes (number of copies of the B (green) allele (0,1,2)) for individual bovine animals within pools.</p></li><br><li><p>Resource Title: Sample Definitions .</p> <p>File Name: XY Data Key.xlsx</p><p>Resource Description: Definitions for each sample (both pools and individual animals).</p></li></ul>
num_resources 3
num_tags 21
title Evaluating accuracy of DNA pool construction based on white blood cell counts