|
| Status |
Public on Dec 07, 2020 |
| Title |
blood_5 |
| Sample type |
genomic |
| |
|
| Source name |
blood from coccygeal vein in the tail
|
| Organism |
Bos taurus |
| Characteristics |
digital dermatitis binary phenotype: case
digital dermatitis quantitative phenotype: 0.25
farm: A
Sex: female
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.
|
| Label |
C-Bio, G-Bio, A-DNP, T-DNP
|
| Label protocol |
According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.
|
| Scan protocol |
Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.
|
| Description |
Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)
|
| Data processing |
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.
|
| |
|
| Submission date |
Oct 07, 2020 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Anita Oberbauer |
| Organization name |
University of California, Davis
|
| Department |
Animal Science Department
|
| Lab |
Oberbauer Lab
|
| Street address |
One Shields Ave.
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL21267 |
| Series (1) |
| GSE159157 |
Genome-wide association studies reveal susceptibility loci for digital dermatitis in Holstein cattle |
|
| Relations |
| Alternative to |
GSM5642180 |
