|
| Status |
Public on Nov 25, 2015 |
| Title |
108-Skin_Blood_Affected |
| Sample type |
genomic |
| |
|
| Source name |
Fibroblast cell line
|
| 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 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 1 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 |
|
