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Sample GSM1949224 Query DataSets for GSM1949224
Status Public on Nov 25, 2015
Title 109D_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 12 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 AB 0.012586 AB 1951.074341 2084.079346
SNP_A-1967418 BB 0.012582 BB 340.795807 1038.014771
SNP_A-1969580 BB 0.006227 BB 1425.380981 3971.975342
SNP_A-4263484 BB 0.000778 BB 602.313171 2046.439453
SNP_A-1978185 AA 0.004555 AA 1714.481201 337.812561
SNP_A-4264431 AB 0.006716 AB 1546.739624 1261.435669
SNP_A-1980898 BB 0.002032 BB 368.055145 989.624939
SNP_A-1983139 AA 0.008858 AA 3598.105469 1192.052734
SNP_A-4265735 AB 0.014054 AB 1843.424194 2108.022949
SNP_A-1995832 BB 0.004088 BB 515.209961 1870.723022
SNP_A-1995893 BB 0.003607 BB 426.715881 2171.585938
SNP_A-1997689 BB 0.002005 BB 797.251587 3430.227783
SNP_A-1997709 AA 0.002709 AA 1659.372437 383.446442
SNP_A-1997896 AA 0.004105 AA 1778.975586 475.791107
SNP_A-1997922 BB 0.010872 BB 666.134155 1160.080200
SNP_A-2000230 AA 0.001592 AA 3277.952881 1041.217041
SNP_A-2000332 AA 0.002720 AA 3147.238525 707.703186
SNP_A-2000337 AA 0.003879 AA 1549.056885 320.363495
SNP_A-2000342 AA 0.000874 AA 3519.063232 964.181152
SNP_A-4268173 AB 0.007544 AB 1076.912231 1182.926025

Total number of rows: 909622

Table truncated, full table size 46137 Kbytes.

Supplementary file Size Download File type/resource
GSM1949224_SB_CID0109D_071908.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM1949224_SB_CID0109D_071908.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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