|
| Status |
Public on Feb 08, 2008 |
| Title |
HGDP-304 |
| Sample type |
genomic |
| |
|
| Source name |
lymphoblastoid cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
Population: Kalash
Country: Pakistan
Region: CENTRAL_SOUTH_ASIA
Gender: Female
|
| Biomaterial provider |
Cell lines from the HGDP-CEPH-Panel derived from ethnically diverse populations; http://www.cephb.fr/HGDP-CEPH-Panel/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted at the Foundation Jean Dausset (CEPH) in Paris using standard protocols.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 1000ng 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 XC3/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
|
| Description |
Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).
|
| Data processing |
Image data was analyzed using Beadstudio 3.1.4 (Illumina).
|
| |
|
| Submission date |
Feb 07, 2008 |
| Last update date |
Feb 08, 2008 |
| Contact name |
J Raphael Gibbs |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institutue on Aging, NIH
|
| Department |
Computational Biology Core
|
| Lab |
Laboratory of Neurogenetics
|
| Street address |
35 Convent Drive, Bldg 35/1A1015, MSC3707
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6433 |
| Series (1) |
| GSE10331 |
Genotype, haplotype and copy number variation in worldwide human populations. |
|
