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Sample GSM1949233 Query DataSets for GSM1949233
Status Public on Nov 25, 2015
Title 104-PreX_Blood_Affected
Sample type genomic
Source name Peripheral blood
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 19 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 0.008119 BB 751.348694 2077.760986
SNP_A-1967418 BB 0.001708 BB 263.000854 819.528564
SNP_A-1969580 BB 0.007505 BB 1132.790405 4702.285156
SNP_A-4263484 BB 0.008368 BB 633.713013 2660.688477
SNP_A-1978185 AB 0.002177 AB 1064.780762 1873.368042
SNP_A-4264431 AB 0.002869 AB 1121.622192 977.031067
SNP_A-1980898 BB 0.014133 BB 270.729553 1229.888794
SNP_A-1983139 AA 0.004250 AA 2133.687012 462.002228
SNP_A-4265735 AB 0.003424 AB 793.229187 797.789368
SNP_A-1995832 BB 0.002275 BB 634.057190 1582.920410
SNP_A-1995893 BB 0.003273 BB 338.001190 1979.173462
SNP_A-1997689 BB 0.006836 BB 645.341370 3388.091797
SNP_A-1997709 AA 0.002127 AA 1582.920410 243.037476
SNP_A-1997896 AB 0.008233 AB 1161.948364 1646.875977
SNP_A-1997922 AB 0.005052 AB 647.239258 639.944092
SNP_A-2000230 AA 0.005175 AA 2984.340576 1057.561523
SNP_A-2000332 AA 0.005233 AA 3062.151123 761.539612
SNP_A-2000337 AA 0.013195 AA 2303.671631 387.431213
SNP_A-2000342 AA 0.004557 AA 3440.961914 904.707703
SNP_A-4268173 AA 0.001024 AA 1568.558960 244.081726

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.

Supplementary file Size Download File type/resource
GSM1949233_SB_CID0104-PreX_072809_EA.CEL.gz 35.2 Mb (ftp)(http) CEL
GSM1949233_SB_CID0104-PreX_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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