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Sample GSM596175 Query DataSets for GSM596175
Status Public on Sep 25, 2010
Title GM17107 (510S)
Sample type genomic
 
Source name lymphoblastoid cell line GM17107
Organism Homo sapiens
Characteristics ethnic group: AA African-American
cell line (coriell id): GM17107
wei id: Wei023
cell type: EBV-transformed lymphoblastoid cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17107
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 0.9874992 0.6091726 0.9984035
rs723490-126_T_R_IFB1161253789:0 BB 0.2611014 0.9174722 0.9363333 0.8354701
rs4955547-123_T_F_IFB1161227890:0 AB 0.1815122 0.4737288 2.079689 0.350002
rs8011562-126_T_R_IFB1161267227:0 NC 0.1112005 0.1491189 0.877394 0.104864
rs9468805-123_B_R_IFB1161276674:0 BB 0.2454607 0.9053549 1.119554 0.9020776
rs2400669-123_T_R_IFB1161184024:0 AB 0.8993196 0.557192 0.8621176 0.4814406
rs1058465-106_T_F_IFB1161110088:0 BB 0.4541007 0.9780631 0.7178944 0.9874623
rs5999-126_T_F_IFB1161234109:0 AA 0.8505118 0.005979697 1.287206 0.00
rs2013854-126_B_R_IFB1161162309:0 AA 0.7400023 0.09949732 0.7145463 0.00
rs16987048-123_B_F_IFB1161149544:0 AA 0.7723933 0.01361379 1.212329 0.00
rs8019730-126_B_F_IFB1161267374:0 NC 0.04651267 0.1297356 0.7459264 0.09786197
rs941986-126_T_F_IFB1161276218:0 NC 0.03946674 0.1705497 0.5846547 0.1107741
rs2294041-126_T_R_IFB1161179340:0 AB 0.7921214 0.5099034 1.04879 0.3980834
rs2232032-98_T_R_IFB1161170583:0 BB 0.8337998 0.9647265 0.6468326 0.978063
rs10005231-126_T_R_IFB1161282566:0 NC 0.0363418 0.2436622 1.035414 0.1453761
rs203674-126_T_F_IFB1161163074:0 NC 0.02650205 0.5363397 0.4422727 0.3756472
rs2271173-126_B_F_IFB1161174408:0 AB 0.866239 0.698795 0.9582359 0.5822049
rs748741-126_B_F_IFB1161257614:0 AA 0.2901492 0.1249845 0.5772401 0.09824944
rs10475542-119_B_R_IFB1161289850:0 AA 0.8014302 0.002018393 2.046249 0.00
rs11191439-126_B_F_IFB1161117943:0 AA 0.9265754 0.00 1.469646 0.00

Total number of rows: 511354

Table truncated, full table size 37594 Kbytes.




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

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