NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1949226 Query DataSets for GSM1949226
Status Public on Nov 25, 2015
Title 111B_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 22 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 0.003793 BB 756.504578 2941.322998
SNP_A-1967418 BB 0.001852 BB 350.202423 902.537109
SNP_A-1969580 BB 0.004569 BB 1311.091064 3733.874756
SNP_A-4263484 AB 0.001128 AB 1922.891968 1356.538818
SNP_A-1978185 AA 0.001357 AA 1512.232910 397.671722
SNP_A-4264431 AB 0.000958 AB 1491.433105 1130.136475
SNP_A-1980898 BB 0.002057 BB 368.205017 877.759949
SNP_A-1983139 AA 0.001223 AA 3568.939941 941.444946
SNP_A-4265735 AA 0.010252 AA 2511.625732 720.703430
SNP_A-1995832 AB 0.001561 AB 1398.092651 1032.121460
SNP_A-1995893 AB 0.001914 AB 1332.011475 1635.891602
SNP_A-1997689 BB 0.005658 BB 714.584106 3857.979492
SNP_A-1997709 AA 0.012138 AA 2193.276367 466.394440
SNP_A-1997896 AA 0.000371 AA 1643.591064 494.168427
SNP_A-1997922 AB 0.015427 AB 1102.871704 818.912781
SNP_A-2000230 AA 0.003325 AA 3008.014893 1058.243164
SNP_A-2000332 AA 0.003035 AA 3466.702637 800.747314
SNP_A-2000337 AA 0.005495 AA 1397.047729 390.205780
SNP_A-2000342 AA 0.008769 AA 4136.213379 1187.903809
SNP_A-4268173 AA 0.004559 AA 2149.303467 409.010254

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM1949226_SB_CID0111B_071908.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM1949226_SB_CID0111B_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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap