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Sample GSM1949216 Query DataSets for GSM1949216
Status Public on Nov 25, 2015
Title 108B_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 4 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 0.001878 BB 637.394836 2968.478271
SNP_A-1967418 AB 0.004230 AB 729.146423 633.424438
SNP_A-1969580 BB 0.011193 BB 867.535645 3459.731201
SNP_A-4263484 AB 0.014401 AB 1518.521240 1021.180969
SNP_A-1978185 AA 0.015727 AA 1948.999512 320.772156
SNP_A-4264431 AA 0.004099 AA 2227.946045 403.224518
SNP_A-1980898 AB 0.001115 AB 832.710999 721.762817
SNP_A-1983139 AA 0.007452 AA 2792.077148 761.845581
SNP_A-4265735 AB 0.008075 AB 1430.765015 1381.421265
SNP_A-1995832 BB 0.002914 BB 456.214478 1591.345337
SNP_A-1995893 BB 0.004421 BB 386.074463 1949.986938
SNP_A-1997689 BB 0.002743 BB 700.876038 3207.950195
SNP_A-1997709 AA 0.001637 AA 1574.559448 341.738739
SNP_A-1997896 AA 0.006966 AA 1545.447998 328.681244
SNP_A-1997922 BB 0.001085 BB 540.907593 1260.879639
SNP_A-2000230 AA 0.007366 AA 3635.076172 1079.461670
SNP_A-2000332 NC 0.032250 AB 3080.398438 3073.873535
SNP_A-2000337 AA 0.001957 AA 1690.349121 320.772156
SNP_A-2000342 AA 0.012581 AA 3934.512207 868.187561
SNP_A-4268173 NC 0.031748 AA 2458.430420 348.621216

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.

Supplementary file Size Download File type/resource
GSM1949216_SB_CID0108B_071908.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM1949216_SB_CID0108B_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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