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| Status |
Public on Aug 31, 2018 |
| Title |
USCF1292 |
| Sample type |
genomic |
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| Source name |
Whole blood
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Whole blood
gender: male
breed: Australian Cattle Dog
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
EDTA-stabilized whole blood or tissue was collected from the Australian Cattle Dogs and Miniature Schnauzers. Genomic DNA was extracted using the illustra Nucleon BACC 2 kit using the manufacturer's recommended protocols (GE Healthcare). This study was conducted with approval from the Animal Ethics Committee at the University of Sydney (approval number N00/9 2009/3/5109 and N00/10-2012/3/5837).
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| Label |
Cy3, Cy5
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| Label protocol |
Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).
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| Hybridization protocol |
Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).
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| Scan protocol |
Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).
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| Description |
Australian Cattle Dog
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| Data processing |
Illumina Genome Studio (GSGT Version 1.9.4) was used to perform genotype calling to obtain the Final Report file.
Column headers for the file "USCF_30JUN18_FinalReport.txt" are: SNP Name, Sample ID, Allele 1 Forward, Allele 2 Forward, Allele 1 Top, Allele 2 Top, Allele 1 AB, Allele2 AB, GC Score, X, Y. This file contains the rawest form of the data available for this data set.
Processed data file includes: Genotype: AA,AB,BB,or NC (no call) and GC_score.
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| Submission date |
Jul 12, 2018 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Tracy Chew |
| Organization name |
University of Sydney
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| Department |
Sydney Informatics Hub
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| Street address |
Merewether Building (H04) City Rd & Butlin Ave
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| City |
Darlington |
| State/province |
NSW |
| ZIP/Postal code |
2008 |
| Country |
Australia |
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| Platform ID |
GPL20953 |
| Series (1) |
| GSE117010 |
Comparison of variant calling pipelines using Illumina CanineHD BeadChip array as the truth dataset |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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