|
| Status |
Public on Jul 12, 2011 |
| Title |
ALL_DS_D17 |
| Sample type |
genomic |
| |
|
| Source name |
ALL, Down syndrome
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
gender: M
disease status: Down syndrome B-precursor ALL
paired sample: Yes, Pair C
|
| 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 at diagnosis and for selected patients at a second timepoint when they were in remission
|
| 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 |
500 ng of genomic DNA was bisulfite converted using the EZ-DNA methylation kit from Zymo Research. 170 ng of freshly bisulfite converted DNA was used to go through denaturation, amplification, fragmentation, and precipitation. Methylated cytidine is labeled with biotinylated guanidine whilst unmethylated cytidine becomes thymidine and is labeled with dinitrophenyl-adenine. Streptavidin-Cy3 and antiDNP-Cy5 are used to fluorescent-tag the target probes.
|
| |
|
| Hybridization protocol |
Processed DNA samples were heated at 95oC for 20 min. Upon cooling, the samples were loaded onto methylation27 chips and allowed to hybridize in RA1 buffer in a 48oC incubation oven for 16 hours. After overnight hybridization, the chips were washed and stained with XC1 to XC3 and coated with XC4.
|
| Scan protocol |
Beadarray scanner software was used and the chips were scanned using the Beadarray scanner 500GX. All parameters were in default setting.
|
| Description |
none
|
| Data processing |
IDAT files were imported into GenomeStudio software version 2009.1. Methylation modules generate the compiled project and gave out average beta value and detection p-value as output.
Average beta value is defined as the ratio of signal from a methylated probe (C not converted to T) relative to the sum of both methylated (C not converted to T) and unmethylated probes (C bisulfite-converted to T) (β value=C/[(T+C)+100]
|
| |
|
| Submission date |
Mar 13, 2010 |
| Last update date |
Jul 12, 2011 |
| Contact name |
Hon-chiu Eastwood Leung |
| E-mail(s) |
[email protected]
|
| 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 |
GPL8490 |
| Series (2) |
| GSE20872 |
Methylation 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 |
|
