|
| Status |
Public on Jan 15, 2012 |
| Title |
PeripheralBlood_DBA_Proband_1382 [NG] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
gDNA from proband 1382
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Peripheral Blood
relationship to proband: Proband
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA is extracted from WBC pelleted from peripheral blood after RBC lysis in 0.15M NH4Cl. WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen). DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.
|
| Label |
cy3
|
| Label protocol |
500 ng of experimental DNA was labeled with Cy3 and 500 ng of reference DNA male/female (Promega) was labeled with Cy5 using the Nimblegen labeling kit according to manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
Commercial Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male and Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA is extracted from WBC pelleted from peripheral blood after RBC lysis in 0.15M NH4Cl. WBC are lysed overnight at 55 °C in WBC lysis solution (Qiagen), and protein precipitated and spun at 4 °C in protein precipitation solution (Qiagen). DNA is preciptated in ethanol, pelleted and resuspended in 10mM Tris EDTA.
|
| Label |
cy5
|
| Label protocol |
500 ng of experimental DNA was labeled with Cy3 and 500 ng of reference DNA male/female (Promega) was labeled with Cy5 using the Nimblegen labeling kit according to manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
DNA mixture was hybridized for 72 hours at 42 °C and washed according to standard Nimblegen protocols
|
| Scan protocol |
Data were scanned on an Agilent 2micron scanner
|
| Description |
Selected samples for which a deletion was identified by SNP genotyping array were confirmed by aCGH on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused
Sample name: 505303A02_DBslide3
|
| Data processing |
Featue extraction and normalization was performed with DEVA software (Nimblegen) according to the standard CGH workflow
|
| |
|
| Submission date |
Aug 24, 2011 |
| Last update date |
Jan 15, 2012 |
| Contact name |
Jason Eli Farrar |
| E-mail(s) |
jefarrar@uams.edu
|
| Phone |
501-603-1224
|
| Organization name |
University of Arkansas for Medical Sciences
|
| Department |
Pediatrics/Hematology-Oncology
|
| Street address |
1 Children's Way, #512-10
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72202 |
| Country |
USA |
| |
|
| Platform ID |
GPL14190 |
| Series (1) |
| GSE31575 |
Ribosomal Protein Gene Deletions in Diamond Blackfan Anemia |
|
