Ag Data Commons
3 files

Data from: Estimation of pool construction and technical error

posted on 2023-12-18, 19:00 authored by John W. Keele, Tara G. McDaneld, Ty E. Lawrence, Jenny S. Jennings

Animals were incorporated into pools in different proportions to estimate error and evaluate factors influencing error. Animals were incorporated into 2 types of pools, sub-pools and super pools. Within phenotype, liver abscess or normal, 16 animals were combined into 4 sub-pools, 4 animals per sub-pool in parts of 1:2:3:4. Sub-pools were constructed based on crushed frozen liver tissue mass. Within phenotype, 4 sub-pools were incorporated into 2 super pools in parts of 1:2:3:4 for super pool 1 and 3:4:1:2 for super pool 2. Super pools were made based on DNA quantity. Errors in DNA quantification would create error in forming super pools from sub-pools and variation in cell content or DNA content of liver tissue would result in error in combining sub-pools from animals.

Animal contributions to sub-pools for livers with abscess sub-pool 1A was 1:2:3:4 parts of 15A, 36A, 35A, and 23A. sub-pool 2A was 1:2:3:4 parts of 42A, 37A, 12A, and 22A. sub-pool 3A was 1:2:3:4 parts of 17A, 1A, 49A, and 48A . sub-pool 4A was 1:2:3:4 parts of 3A, 20A, 16A, and 13A. Each part was 0.1 g of pulverized frozen liver tissue. Animal contributions to livers without abscess sub-pool 1N was 1:2:3:4 parts of 46N, 23N, 17N, and 12N. sub-pool 2N was 1:2:3:4 parts of 1N, 31N, 6N, and 48N. sub-pool 3N was 1:2:3:4 parts of 36N, 43N, 32N, and 13N. sub-pool 4N was 1:2:3:4 parts of 34N, 19N, 41N, and 50N. Sub-pool contributions to super pools for livers with abscess super pool 1A was:1:2:3:4 parts sub-pool 1A, sub-pool 2A, sub-pool 3A, and sub-pool 4A. super pool 2A was 3:4:1:2 parts sub-pool 1A, sub-pool 2A, sub-pool 3A, and sub-pool 4A. Sub-pool contributions to super pools for livers with without abscess super pool 1N was:1:2:3:4 parts sub-pool 1N, sub-pool 2N, sub-pool 3N, and sub-pool 4N. super pool 2N was 3:4:1:2 parts sub-pool 1N, sub-pool 2N, sub-pool 3N, and sub-pool 4N.

Funded by the USDA Agricultural Research Service, Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production/ 3040-31000-100-000-D

Resources in this dataset:

  • Resource Title: xy data for individual animals.

    File Name: xyIndividuals.csv.gz

    Resource Description: X (red) and Y (green) intensity data for 32 animals. There are 64 columns, an X and Y column for each animal

  • Resource Title: Genotypes, Number of copies of B allele for BovineHD 770K.

    File Name: g.csv.gz

    Resource Description: Values are 0, 1 and 2 for 32 animals and 777,962 SNP, DNA was extracted from pulverized frozen liver tissue

  • Resource Title: x and y data for pools.

    File Name: xyPools.csv.gz

    Resource Description: X (red) and Y (green) intensity for 12 pools. There are 2 columns per pool, first is X followed by Y. First 8 columns are super pools and second 16 are sub-pools. Examples superPool.1A.X is superPool 1 for abscess livers and X intensity sub-pool.1A.Y is sub-pools 1 for abscess livers and Y intensity


USDA-ARS: 3040-31000-100-000-D


Data contact name

Keele, John

Data contact email


Ag Data Commons

Intended use

Data were generated to estimate pooling errors.

Temporal Extent Start Date



  • Not specified

Geographic Coverage


Geographic location - description

western Texas

ISO Topic Category

  • biota
  • farming

Ag Data Commons Group

  • AgBioData

National Agricultural Library Thesaurus terms

animals; phenotype; liver abscess; liver; DNA; genotype; alleles; single nucleotide polymorphism; breeding value; prediction; Biological Sciences; Breeding and Genetic Improvement; Animal Science and Animal Products

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 101

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Keele, John W.; McDaneld, Tara G.; Lawrence, Ty E.; Jennings, Jenny S. (2021). Data from: Estimation of pool construction and technical error. Ag Data Commons.

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