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Sample GSM1949215 Query DataSets for GSM1949215
Status Public on Nov 25, 2015
Title 108A_Blood_Obligate carrier
Sample type genomic
 
Source name Saliva
Organism Homo sapiens
Characteristics gender: Male
clinical status: Obligate carrier
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 27 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 0.007435 BB 809.885925 2971.537109
SNP_A-1967418 AB 0.002865 AB 627.930298 526.696106
SNP_A-1969580 BB 0.002806 BB 1189.466431 3631.756592
SNP_A-4263484 AB 0.001718 AB 1942.138794 1311.678589
SNP_A-1978185 AA 0.003441 AA 1403.920654 401.756622
SNP_A-4264431 AB 0.010794 AB 1695.377808 1102.208130
SNP_A-1980898 BB 0.004720 BB 327.716278 850.054138
SNP_A-1983139 AA 0.004764 AA 3152.332031 1008.193787
SNP_A-4265735 AA 0.010231 AA 2204.259766 640.721069
SNP_A-1995832 BB 0.003722 BB 501.928680 1839.285522
SNP_A-1995893 BB 0.001499 BB 436.015686 2117.058594
SNP_A-1997689 BB 0.002322 BB 787.593262 3310.156006
SNP_A-1997709 AA 0.005167 AA 1471.974976 298.621704
SNP_A-1997896 AA 0.000564 AA 1613.346436 499.179199
SNP_A-1997922 BB 0.006500 BB 538.813110 1414.687134
SNP_A-2000230 AA 0.004990 AA 3333.257080 1331.225830
SNP_A-2000332 AB 0.002852 AB 2403.363037 2364.090576
SNP_A-2000337 AA 0.002102 AA 1526.878052 364.791718
SNP_A-2000342 AA 0.004836 AA 3505.243896 1123.902710
SNP_A-4268173 AB 0.005136 AB 1141.124634 1213.175903

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM1949215_SB_CID0108A_071708.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM1949215_SB_CID0108A_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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