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Sample GSM1949225 Query DataSets for GSM1949225
Status Public on Nov 25, 2015
Title 111A_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 21 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
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.000885 BB 665.866150 3031.245850
SNP_A-1967418 BB 0.005560 BB 372.241730 825.611816
SNP_A-1969580 BB 0.010760 BB 1508.935059 4002.132324
SNP_A-4263484 BB 0.007009 BB 636.236389 1841.868164
SNP_A-1978185 AA 0.001917 AA 1499.992920 328.582581
SNP_A-4264431 BB 0.002559 BB 604.195984 1585.610107
SNP_A-1980898 BB 0.005178 BB 419.111145 868.246460
SNP_A-1983139 AA 0.002711 AA 3711.772949 1001.722534
SNP_A-4265735 AA 0.007284 AA 2698.454834 585.807190
SNP_A-1995832 BB 0.005109 BB 607.295166 1859.719604
SNP_A-1995893 BB 0.008656 BB 530.049255 2309.099365
SNP_A-1997689 BB 0.006220 BB 647.786560 3069.085938
SNP_A-1997709 AA 0.001961 AA 1715.391235 381.303314
SNP_A-1997896 AA 0.002512 AA 1756.680176 515.800415
SNP_A-1997922 NC 0.020752 BB 655.948242 1612.949951
SNP_A-2000230 AA 0.002273 AA 3093.408936 1038.049805
SNP_A-2000332 AA 0.010600 AA 3216.619385 1057.680298
SNP_A-2000337 AA 0.005908 AA 1655.407959 293.478485
SNP_A-2000342 AA 0.010303 AA 3477.939453 1202.885254
SNP_A-4268173 AB 0.006812 AB 1076.653320 956.313416

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.




Supplementary file Size Download File type/resource
GSM1949225_SB_CID0111A_071908.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM1949225_SB_CID0111A_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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