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Sample GSM1953824 Query DataSets for GSM1953824
Status Public on Nov 25, 2015
Title UNK-344-USAB2_Peripheral blood_Affected_rep2
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 peripheral blood or fibroblast cell lines using the Qiagen Gentra Puregene Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Picogreen assay.
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 1 in published pedigree B
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 0.1.
Genotype calls (AA, AB, BB, and NoCall) for both unfiltered SNP list (all 909622 SNPs) and filtered SNP list (678442 SNPs used for haplotype comparison)
Submission date Nov 24, 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)
GSE75349 A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency (Family B)
GSE75358 A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency

Data table header descriptions
VALUE Genotype call

Data table
SNP_A-2131660 AB
SNP_A-1967418 BB
SNP_A-1969580 BB
SNP_A-4263484 BB
SNP_A-1978185 AA
SNP_A-4264431 AA
SNP_A-1980898 BB
SNP_A-1983139 AA
SNP_A-4265735 AA
SNP_A-1995832 AB
SNP_A-1995893 AB
SNP_A-1997689 BB
SNP_A-1997709 AA
SNP_A-1997896 AA
SNP_A-1997922 AB
SNP_A-2000230 AA
SNP_A-2000332 AA
SNP_A-2000337 AA
SNP_A-2000342 AA
SNP_A-4268173 AA

Total number of rows: 909622

Table truncated, full table size 15136 Kbytes.

Supplementary file Size Download File type/resource
GSM1953824_EA14165_381564_GENOMEWIDESNP_6_UNK-344-USAB2.CEL.gz 29.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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