|
| Status |
Public on Jul 12, 2011 |
| Title |
DS ALL (4256134252_A) |
| Sample type |
genomic |
| |
|
| Source name |
ALL, Down Syndrome
|
| Organism |
Homo sapiens |
| Characteristics |
raw data: raw6
raw file sample id: 4256134252_A
tissue: bone marrow
gender: Female
disease status: ALL, Down Syndrome
|
| Treatment protocol |
No additional treatments were performed prior to extract preparation.
|
| Growth protocol |
Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with B-precursor acute lymphoblastic leukemia and control patients without leukemia.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA from Ficoll-enriched cryopreserved bone marrow samples was performed using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
|
| Description |
Genomic DNA extracted from bone marrow was genotyped using the Infinium Human 3700Duo BeadChips (Illumina).
|
| Data processing |
Genomic DNA extracted from bone marrow was genotyped using Infinium Human370-Duo Genotyping BeadChips (Illumina). GenomeStudio v2009.1, the Genotyping Module v1.0 by Illumina Inc was used with no normalization and the following processing steps: 1) Gen Call Threshold = 0.15, 2) Import cluster from the cluster file: HumanCNV370v1_C.egt
|
| |
|
| Submission date |
Mar 26, 2010 |
| Last update date |
Jul 12, 2011 |
| Contact name |
Hon-chiu Eastwood Leung |
| E-mail(s) |
exleung@txccc.org
|
| Phone |
832-824-4373
|
| Fax |
832-825-4038
|
| URL |
http://www.txccc.org/content.cfm?content_id=1405
|
| Organization name |
Baylor College of Medicine
|
| Department |
Pediatrics
|
| Lab |
Genomics and Proteomics Core Laboratory
|
| Street address |
1102 Bates Street Room C1030.09
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6986 |
| Series (2) |
| GSE21091 |
SNP data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases and controls |
| GSE21094 |
Genomic profiling in Down syndrome pediatric acute lymphoblastic leukemia |
|
