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Sample GSM1949214 Query DataSets for GSM1949214
Status Public on Nov 25, 2015
Title 104C_Blood_Healthy
Sample type genomic
Source name Saliva
Organism Homo sapiens
Characteristics gender: Male
clinical status: Healthy
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 20 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 0.008463 BB 724.544434 2485.609375
SNP_A-1967418 BB 0.002454 BB 336.081116 801.821289
SNP_A-1969580 BB 0.006247 BB 974.229248 3596.073242
SNP_A-4263484 BB 0.007909 BB 488.421326 1812.325684
SNP_A-1978185 AB 0.001111 AB 1259.715332 1909.596558
SNP_A-4264431 BB 0.002418 BB 529.849182 1640.147095
SNP_A-1980898 BB 0.001360 BB 380.077911 970.888672
SNP_A-1983139 NC 0.021112 AA 2311.099854 680.751038
SNP_A-4265735 AB 0.005989 AB 1402.976685 1471.424927
SNP_A-1995832 BB 0.001221 BB 496.341492 1677.197754
SNP_A-1995893 BB 0.001289 BB 432.431976 2003.817993
SNP_A-1997689 BB 0.004821 BB 819.835449 3202.161377
SNP_A-1997709 AA 0.003247 AA 1536.574585 316.579651
SNP_A-1997896 AA 0.008102 AA 1399.746582 371.653870
SNP_A-1997922 BB 0.000877 BB 538.760132 1164.774414
SNP_A-2000230 AA 0.001890 AA 3399.869873 1153.038818
SNP_A-2000332 AA 0.004226 AA 3427.001953 685.998474
SNP_A-2000337 AA 0.005458 AA 1820.667725 289.948700
SNP_A-2000342 AA 0.011124 AA 3926.936523 1290.726440
SNP_A-4268173 AB 0.014146 AB 1539.453247 1354.267822

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.

Supplementary file Size Download File type/resource
GSM1949214_SB_CID0104C_071708.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM1949214_SB_CID0104C_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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