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Status |
Public on Feb 21, 2020 |
Title |
Whole blood, JA17 |
Sample type |
genomic |
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Source name |
Jugular vein
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Organism |
Bos indicus |
Characteristics |
gender: Female breed: Ji'an cattle altitude (m): 200 longitude: E116°00′ latitude: N26°28′ tissue: Whole blood
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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.
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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).
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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).
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Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
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Description |
Genomic DNA extracted from whole blood was genotyped using BovineHD Genotyping BeadChip (Illumina).
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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
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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 |
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