|
| Status |
Public on Dec 29, 2009 |
| Title |
256735-ES-rehyb-13-080930 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MspI: CD34+ selected cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
sample source: Infant, normal, CD34+ selected cord blood
|
| 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 |
HpaII: CD34+ selected cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
sample source: Infant, normal, CD34+ selected cord blood
|
| 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 |
CD19+-2
|
| 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 |
Dec 28, 2009 |
| Last update date |
Dec 28, 2009 |
| Contact name |
Eric Stephen Schafer |
| E-mail(s) |
eschafe1@jhmi.edu
|
| Phone |
(410) 955-8817
|
| Fax |
(410) 955-8897
|
| Organization name |
Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
|
| Department |
Pediatrics and Oncology
|
| Lab |
Patrick Brown Laboratory
|
| Street address |
CRB1, Room 252a, 1650 Orleans St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (1) |
| GSE19671 |
Promoter hypermethylation in MLL-r leukemia: biology and therapeutic targeting |
|
