|
| Status |
Public on Apr 01, 2008 |
| Title |
ALL1_HELP_Replicate3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ALL1_replicate3
|
| Organism |
Homo sapiens |
| Characteristics |
Female
Acute Lymphoblastic Leukemia with t(9;22)(q34;q11)
Early Pre-B ALL with co-expression of CD33 and CD13
BCR-ABL p190 (e1a2)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
|
| Label |
Cy5
|
| Label protocol |
Random 9-mers pre-labeled with Cy5
|
| |
|
| Channel 2 |
| Source name |
ALL1_Replicate3
|
| Organism |
Homo sapiens |
| Characteristics |
Female
Acute Lymphoblastic Leukemia with t(9;22)(q34;q11)
Early Pre-B ALL with co-expression of CD33 and CD13
BCR-ABL p190 (e1a2)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with MspI and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
|
| Label |
Cy3
|
| Label protocol |
Random 9-mers pre-labeled with Cy3
|
| |
|
| |
| Hybridization protocol |
See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
|
| Scan protocol |
scanned using a GenePix 4000B scanner (Axon Instruments) (See Selzer RR, et al. Genes Chromosomes Cancer 44: 305-319.)
|
| Description |
All samples for microarray hybridization were processed at the Roche NimbleGen Service Laboratory.
|
| Data processing |
Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data.
|
| |
|
| Submission date |
Mar 19, 2008 |
| Last update date |
Mar 24, 2008 |
| Contact name |
Maria Eugenia Figueroa |
| E-mail(s) |
mef162@miami.edu
|
| Organization name |
University of Miiami
|
| Department |
Human Genetics
|
| Lab |
Maria Figueroa
|
| Street address |
1501 NW 10th Ave, BRB 709A, Locator code C227
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (1) |
| GSE10894 |
DNA methylation by HELP for Integrative epigenomic study in leukemia samples |
|
