|
| Status |
Public on Feb 21, 2020 |
| Title |
Whole blood, WN12 |
| Sample type |
genomic |
| |
|
| Source name |
Jugular vein
|
| Organism |
Bos taurus |
| Characteristics |
gender: Female
breed: Weining cattle
altitude (m): 1900
longitude: E104°17'
latitude: N26°52'
tissue: Whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA from the anti-coagulant treated whole blood was performed using proteinase K and standard phenol-chloroform extraction.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
|
| Description |
Genomic DNA extracted from whole blood was genotyped using BovineHD Genotyping BeadChip (Illumina).
|
| Data processing |
Genomic DNA extracted from whole blood was genotyped using BovineHD Genotyping BeadChip (Illumina).
[matrix.txt] Genotype: AA,AB,BB,or NC (no call), Log_R_Ratio, B_Allele_Freq
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Feb 21, 2020 |
| Contact name |
Yaran Zhang |
| E-mail(s) |
zhang_ya_ran@126.com
|
| Phone |
18853115768
|
| Organization name |
Shandong Acdemy of Agricultural Sciences
|
| Street address |
North industrial road
|
| City |
Ji'nan |
| ZIP/Postal code |
250100 |
| Country |
China |
| |
|
| Platform ID |
GPL21267 |
| Series (1) |
| GSE142218 |
Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle |
|
