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Sample GSM596184 Query DataSets for GSM596184
Status Public on Sep 25, 2010
Title GM17116 (510S)
Sample type genomic
 
Source name lymphoblastoid cell line GM17116
Organism Homo sapiens
Characteristics ethnic group: AA African-American
cell line (coriell id): GM17116
wei id: Wei063
cell type: EBV-transformed lymphoblastoid cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17116
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purchased from the Coriell Cell Repository (Camden, NJ), which was extracted from the cell cultures in the Repositories
Label C-Bio and A-DNP
Label protocol 750 ng of high quality DNA samples are denatured and neutralized, and then are isothermally amplified in an overnight step. The amplified product is fragmented by a controlled enzymatic process that does not require gel electrophoresis. The process uses end-point fragmentation to avoid overfragmenting the sample. After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4ÂșC, and resuspended in a hybridization buffer.
 
Hybridization protocol Samples are applied to each BeadChip. The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50mers (covalently linked to one of over 500,000 bead types) during hybridization. One bead type corresponds to each allele per SNP locus. Unhybridized and non-specifically hybridized DNA is washed away. The chip undergoes staining and extension in capillary flow-through chambers. Singlebase extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates detectable labels on the BeadChip and determines the genotype call for the sample.
Scan protocol The Illumina BeadArray Reader scans the BeadChip, using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores.
Description Genomic DNA extracted from lymphoblastoid cell line was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).
Data processing Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using Infinium HumanExon510S-2 DNA Analysis Kit (Illumina).
 
Submission date Sep 21, 2010
Last update date Sep 24, 2010
Contact name Liewei Wang
E-mail(s) wang.liewei@mayo.edu
Phone 507-284-5264
Fax 507-284-4455
URL http://mayoresearch.mayo.edu/staff/wang_l2.cfm
Organization name Mayo Clinic
Department Molecular Pharmacology and Experimental Therapeutics
Street address 200 First street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL6988
Series (2)
GSE24245 Genome-wide SNP array data from Human Variation Panel by Illumina 510S
GSE24277 Human Variation Panel: Gene Expression and Genotype

Data table header descriptions
ID_REF
VALUE genotype call
Score
Theta
R
B Allele Freq

Data table
ID_REF VALUE Score Theta R B Allele Freq
rs3823184-107_T_F_IFB1161211720:0 BB 0.4478033 0.9814265 0.6249681 0.9914169
rs723490-126_T_R_IFB1161253789:0 AA 0.816741 0.03674095 0.5397384 0.01575837
rs4955547-123_T_F_IFB1161227890:0 AB 0.8099243 0.6640056 1.428797 0.5176448
rs8011562-126_T_R_IFB1161267227:0 AA 0.914583 0.03493394 0.7429228 0.007683144
rs9468805-123_B_R_IFB1161276674:0 BB 0.9184136 0.9831462 1.335016 0.9980706
rs2400669-123_T_R_IFB1161184024:0 BB 0.8993196 0.9791648 0.7821631 0.9899285
rs1058465-106_T_F_IFB1161110088:0 BB 0.4541007 0.9813976 1.322239 0.9913342
rs5999-126_T_F_IFB1161234109:0 AA 0.8505118 0.01332271 1.217444 0.002402375
rs2013854-126_B_R_IFB1161162309:0 AB 0.7266632 0.7476913 0.9510496 0.4645431
rs16987048-123_B_F_IFB1161149544:0 AA 0.7723933 0.02734185 1.649117 0.008962956
rs8019730-126_B_F_IFB1161267374:0 AB 0.8946313 0.5502138 0.7375138 0.4491034
rs941986-126_T_F_IFB1161276218:0 BB 0.847701 0.9711948 0.7841313 0.9788464
rs2294041-126_T_R_IFB1161179340:0 AB 0.8530563 0.6435609 1.308008 0.5075751
rs2232032-98_T_R_IFB1161170583:0 BB 0.8337998 0.9772621 0.5664346 0.9949718
rs10005231-126_T_R_IFB1161282566:0 AA 0.810324 0.04881132 0.8622146 0.004481118
rs203674-126_T_F_IFB1161163074:0 AA 0.8674639 0.02175614 0.3510026 0.00
rs2271173-126_B_F_IFB1161174408:0 AB 0.866239 0.62198 0.8126937 0.4849654
rs748741-126_B_F_IFB1161257614:0 BB 0.9073936 0.9870761 0.6852603 1
rs10475542-119_B_R_IFB1161289850:0 AA 0.8014302 0.00283367 1.836672 0.0002030191
rs11191439-126_B_F_IFB1161117943:0 AA 0.9265754 0.002298062 1.185961 0.0008027119

Total number of rows: 511354

Table truncated, full table size 37677 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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