|
| 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 |
|
