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Sample GSM1949223 Query DataSets for GSM1949223
Status Public on Nov 25, 2015
Title 109B_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 11 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 0.009425 AB 2666.574219 2834.285889
SNP_A-1967418 BB 0.000774 BB 341.611969 869.523621
SNP_A-1969580 BB 0.002639 BB 1150.167236 3617.088623
SNP_A-4263484 BB 0.005889 BB 569.041687 1769.842285
SNP_A-1978185 AA 0.010061 AA 1835.232788 504.659668
SNP_A-4264431 AB 0.006026 AB 1257.503174 1114.399414
SNP_A-1980898 BB 0.004060 BB 322.302155 979.127014
SNP_A-1983139 AA 0.008431 AA 3450.363770 687.733826
SNP_A-4265735 AB 0.001728 AB 1559.936035 1585.247925
SNP_A-1995832 BB 0.004348 BB 435.078003 1631.796387
SNP_A-1995893 BB 0.014792 BB 442.775024 2395.101807
SNP_A-1997689 BB 0.005764 BB 717.056885 3865.728760
SNP_A-1997709 AA 0.004295 AA 1397.750854 360.026733
SNP_A-1997896 AA 0.001530 AA 1701.076538 563.989319
SNP_A-1997922 BB 0.002975 BB 546.743408 1331.862915
SNP_A-2000230 AA 0.010187 AA 3368.022705 1449.440918
SNP_A-2000332 NC 0.036691 AA 3151.897705 1274.459717
SNP_A-2000337 AA 0.007846 AA 2058.158936 317.427277
SNP_A-2000342 AA 0.007857 AA 3698.114258 841.098083
SNP_A-4268173 AB 0.002248 AB 1171.396362 1171.672729

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.

Supplementary file Size Download File type/resource
GSM1949223_SB_CID0109B_071908.CEL.gz 25.3 Mb (ftp)(http) CEL
GSM1949223_SB_CID0109B_071908.birdseed-v2.chp.gz 12.7 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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