|
| Status |
Public on Mar 28, 2014 |
| Title |
BJ [CNV] |
| Sample type |
genomic |
| |
|
| Source name |
Normal Human BJ fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
individual: control
cell type: BJ fibroblast
passage: control
|
| Treatment protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified with Qiagen Blood and Tissue DNA kit.
|
| Label |
biotin
|
| Label protocol |
The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
|
| Description |
Normal Human BJ fibroblast
|
| Data processing |
For detecting CNV calls, the Affymetrix Genotyping Console 4.1.1 algorithm was used. CNV locations are based on the human genome assembly of March 2006 (hg18). Samples were normalized to Affymetrix HapMap reference dataset hybridized on the same platform. For CNV calls, regional GC correction, 10-kilobase (KB) cut-off value, and a minimum of ten markers were used as analysis configurations. All samples passed quality control requirements. See supplementary file linked to Series record.
|
| |
|
| Submission date |
May 14, 2013 |
| Last update date |
Mar 28, 2014 |
| Contact name |
Hu Li |
| E-mail(s) |
li.hu@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology & Experimental Therapeutics
|
| Lab |
Systems Biology and Pharmacology
|
| Street address |
200 First Street, Gonda Building G19-408
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55904 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE46848 |
The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming |
| GSE55395 |
The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming [Affymetrix] |
|
