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Sample GSM1949235 Query DataSets for GSM1949235
Status Public on Nov 25, 2015
Title 109-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 9 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 AB 0.015356 AB 1469.733398 1335.768433
SNP_A-1967418 BB 0.000628 BB 284.952545 794.557983
SNP_A-1969580 BB 0.028435 BB 1462.511230 5045.015625
SNP_A-4263484 BB 0.004749 BB 637.194702 2508.947754
SNP_A-1978185 AA 0.014887 AA 1095.557617 302.278015
SNP_A-4264431 AA 0.002441 AA 1831.084961 383.905975
SNP_A-1980898 BB 0.012854 BB 300.802246 1253.929688
SNP_A-1983139 AA 0.002885 AA 2243.639160 523.436523
SNP_A-4265735 AB 0.005021 AB 859.128296 963.108643
SNP_A-1995832 BB 0.017378 BB 823.188599 1761.720093
SNP_A-1995893 BB 0.002957 BB 339.285950 2067.524658
SNP_A-1997689 BB 0.008348 BB 587.929077 3414.886230
SNP_A-1997709 AA 0.000627 AA 1616.444458 268.254059
SNP_A-1997896 AA 0.005774 AA 1762.076904 568.753784
SNP_A-1997922 BB 0.009382 BB 375.979218 819.485107
SNP_A-2000230 AA 0.005249 AA 2716.733643 1030.245117
SNP_A-2000332 AA 0.016598 AA 3418.210449 706.734436
SNP_A-2000337 AA 0.000628 AA 1852.049561 326.098907
SNP_A-2000342 AA 0.006077 AA 3545.058594 998.494690
SNP_A-4268173 AA 0.003258 AA 1415.185059 272.835175

Total number of rows: 909622

Table truncated, full table size 46158 Kbytes.




Supplementary file Size Download File type/resource
GSM1949235_SB_CID0109-PreX_072809_EA.CEL.gz 34.7 Mb (ftp)(http) CEL
GSM1949235_SB_CID0109-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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