|
| Status |
Public on Aug 05, 2009 |
| Title |
MDS#5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Bone marrow CD34- fraction
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 43y
disease: Myelodysplasia
treatment: none
time: baseline
tissue: bone marrow
cell type: CD34- fraction
restriction enzyme: MspI
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with either MspI or 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 |
Cy3
|
| Label protocol |
Random 9-mers pre-labeled with either Cy3 or Cy5.
|
| |
|
| Channel 2 |
| Source name |
Bone marrow CD34- fraction
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34- fraction
gender: Male
age: 43y
disease: Myelodysplasia
treatment: none
time: baseline
tissue: bone marrow
restriction enzyme: HpaII
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with either MspI or 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 either Cy3 or Cy5.
|
| |
|
| |
| 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 |
Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in 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.
|
| Description |
MspI representation of genomic DNA vs. HpaII representation of genomic DNA.
|
| 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 (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.
|
| |
|
| Submission date |
Jul 31, 2009 |
| Last update date |
Aug 05, 2009 |
| 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) |
| GSE17328 |
Genome-wide DNA methylation in MDS/secondary AML and de novo AML |
|
