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Sample GSM1949234 Query DataSets for GSM1949234
Status Public on Nov 25, 2015
Title 108-Skin_Blood_Affected
Sample type genomic
Source name Fibroblast cell line
Organism Homo sapiens
Characteristics gender: Male
clinical status: Affected
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 1 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 0.034735 BB 916.467651 1819.078003
SNP_A-1967418 BB 0.002104 BB 328.312134 856.056824
SNP_A-1969580 BB 0.007728 BB 1176.939087 4119.541016
SNP_A-4263484 BB 0.005137 BB 620.930298 2536.074463
SNP_A-1978185 AA 0.008750 AA 1322.788696 395.131836
SNP_A-4264431 AB 0.003286 AB 1214.149292 1086.560669
SNP_A-1980898 AB 0.000564 AB 770.278320 666.564453
SNP_A-1983139 AA 0.012433 AA 1728.020264 413.781921
SNP_A-4265735 AB 0.003393 AB 757.729614 946.485657
SNP_A-1995832 BB 0.014025 BB 803.491211 1695.449463
SNP_A-1995893 BB 0.002141 BB 352.688141 2065.916504
SNP_A-1997689 BB 0.008313 BB 835.920410 3417.662598
SNP_A-1997709 AA 0.009532 AA 1263.812500 257.762329
SNP_A-1997896 AA 0.012144 AA 1558.998535 648.127380
SNP_A-1997922 BB 0.004302 BB 391.295959 916.963135
SNP_A-2000230 AA 0.006267 AA 3245.081543 1132.021606
SNP_A-2000332 AA 0.007479 AA 2736.389404 650.186523
SNP_A-2000337 AA 0.003342 AA 1919.866211 399.582886
SNP_A-2000342 AA 0.004676 AA 3578.218506 975.946472
SNP_A-4268173 AB 0.012374 AB 1048.506714 918.215759

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.

Supplementary file Size Download File type/resource
GSM1949234_SB_CID0108-Skin_072809_EA.CEL.gz 34.6 Mb (ftp)(http) CEL
GSM1949234_SB_CID0108-Skin_072809_EA.birdseed-v2.chp.gz 13.2 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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