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Sample GSM1949213 Query DataSets for GSM1949213
Status Public on Nov 25, 2015
Title 104B_Blood_Obligate carrier
Sample type genomic
Source name Saliva
Organism Homo sapiens
Characteristics gender: Male
clinical status: Obligate carrier
Treatment protocol None
Growth protocol Fibroblasts were grown from skin biopsies according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from saliva, peripheral blood, or fibroblast cell lines using the QIAamp DNA Blood Mini Kit or QIAamp DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label Biotin
Label protocol DNA was restriction digested, ligated to adaptors, PCR amplified, fragmented, labeled, and loaded onto arrays as per the Affymetrix protocol.
Hybridization protocol Arrays were hybridized in the Affymetrix GeneChip Hybridization Oven 640 and washed using the Affymetrix GeneChip Fluidics Station 450 as per the Affymetrix protocol.
Scan protocol Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G as per the Affymetrix protocol.
Description Subject 29 in published pedigree A
Data processing The array image (DAT file) was acquired and converted to a CEL file using Affymetrix GeneChip Operating Software (GCOS v1.4). Genotype calling was performed using Birdseed v2 within Affymetrix Genotyping Console v3.0, with a confidence threshold of 0.02.
primary data description: Genotype calls (AA, AB, BB, and NoCall) and Birdseed confidence values for both unfiltered SNP list (all 909622 SNPs) and filtered SNP list (145751 SNPs used for linkage scans)
Submission date Nov 23, 2015
Last update date Nov 25, 2015
Contact name Raif S. Geha
Organization name Boston Children's Hospital
Department Division of Immunology
Lab Geha Laboratory
Street address 1 Blackfan Circle, Karp 10
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL6801
Series (2)
GSE75314 A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency (Family A)
GSE75358 A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency

Data table header descriptions

Data table
SNP_A-2131660 BB 0.003584 BB 746.239929 2904.289551
SNP_A-1967418 BB 0.007764 BB 375.394165 799.528687
SNP_A-1969580 BB 0.009903 BB 1200.844482 3256.696289
SNP_A-4263484 BB 0.002782 BB 550.899109 1889.592773
SNP_A-1978185 AA 0.001571 AA 1651.192993 378.313171
SNP_A-4264431 AB 0.016713 AB 1797.514282 1177.910522
SNP_A-1980898 BB 0.005776 BB 408.336792 839.634949
SNP_A-1983139 AA 0.008626 AA 2724.981934 792.831604
SNP_A-4265735 AA 0.004433 AA 2374.979248 642.652832
SNP_A-1995832 BB 0.003750 BB 464.008636 1751.620605
SNP_A-1995893 BB 0.003116 BB 411.314392 2109.427734
SNP_A-1997689 BB 0.000638 BB 756.692505 3411.244629
SNP_A-1997709 AA 0.002785 AA 1453.091187 337.110840
SNP_A-1997896 AB 0.006288 AB 1083.173462 1572.558716
SNP_A-1997922 AB 0.002162 AB 834.976257 790.660645
SNP_A-2000230 AA 0.006664 AA 3351.143555 1375.163574
SNP_A-2000332 AA 0.005392 AA 2974.850830 730.300415
SNP_A-2000337 AA 0.006579 AA 2011.421875 331.045044
SNP_A-2000342 AA 0.002493 AA 3673.776123 1108.033813
SNP_A-4268173 AB 0.003867 AB 1226.676880 1259.375610

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM1949213_SB_CID0104B_071708.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM1949213_SB_CID0104B_071708.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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