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| Status |
Public on Dec 31, 2022 |
| Title |
GenomicDNA_Control_USCF1762 |
| Sample type |
genomic |
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| Source name |
Whole blood_healthy
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| Organism |
Canis lupus familiaris |
| Characteristics |
sample group: healthy control
tissue: Whole blood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from whole blood samples using the phenol-chloroform salting-out method as previously described (Miller et al. 1988), or the spin column-based nucleic acid purification method according to the manufacturer’s protocol (QIAamp; QIAGEN, Melbourne, VIC, Australia).
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| Label |
cy3, cy5
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| Label protocol |
According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips
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| Hybridization protocol |
According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips
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| Scan protocol |
According to the service provider GeneSeek, NE, http://genomics.neogen.com/en/beadchips
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| Data processing |
The raw data (idat) files were provided as a service by GeneSeek (Lincoln, NE, USA). The processed file was presented in the format of ped and map files since the processed matrix could not be obtained from Geneseek (Lincoln, NE, USA), without an additional charge. The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory: Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), and phenotype. Genotypes (column 7 onwards) should also be white-space delimited; they can be any character (e.g. 1,2,3,4 or A,C,G,T or anything else) except 0 which is, by default, the missing genotype character. All markers should be biallelic. All SNPs (whether haploid or not) must have two alleles specified. Either Both alleles should be missing (i.e. 0) or neither. No header row should be given. The MAP describes a single marker and must contain exactly 4 columns: chromosome (1-22, X, Y or 0 if unplaced), snp identifier, Genetic distance (morgans), and Base-pair position (bp units). The MAP file must therefore contain as many markers as are in the PED file. The markers in the PED file do not need to be in genomic order: (i.e. the order MAP file should align with the order of the PED file markers). Note: Idat files could no longer be obtained from the service provider for 9 of the 163 healthy controls (thus, 154 healthy control samples are included in the records).
value definition: Genotype 11,12,22,or 00 (no call)
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| Submission date |
Aug 02, 2017 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Annie Pan |
| Organization name |
University of Sydney
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| Department |
School of Life and Environmental Sciences
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| Street address |
Reagent Crescent
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| City |
CAMPERDOWN |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
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| Platform ID |
GPL20953 |
| Series (1) |
| GSE102154 |
Cerebellar abiotrophy in working Kelpies with a later clinical onset |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM2729008_3999355026_R04C01_Grn.idat.gz |
1.3 Mb |
(ftp)(http) |
IDAT |
| GSM2729008_3999355026_R04C01_Red.idat.gz |
1.3 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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