|
| Status |
Public on Jul 31, 2010 |
| Title |
UPN1 (Methylation) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MCL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
restriction enzyme: MspI representation of genomic DNA
sample type: MCL cell line
cell line: UPN1
|
| Biomaterial provider |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit according to the manufacturer instructions (Qiagene). Genomic DNA from RNeasy (Qiagen) flow-through was first precipitated with Ethanol, then purified following proteinase K digestion and standard phenol/choloroform 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 Cy5 or Cy3
|
| |
|
| Channel 2 |
| Source name |
MCL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
restriction enzyme: HpaII representation of genomic DNA
sample type: MCL cell line
cell line: UPN1
|
| Biomaterial provider |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit according to the manufacturer instructions (Qiagene). Genomic DNA from RNeasy (Qiagen) flow-through was first precipitated with Ethanol, then purified following proteinase K digestion and standard phenol/choloroform 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 Cy5 or 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 |
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 |
Genomic DNA from blood was isolated using Puregene Cell and Tissue Kit
|
| 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 01, 2009 |
| Last update date |
Dec 01, 2009 |
| Contact name |
Samir Parekh |
| E-mail(s) |
sparekh@aecom.yu.edu
|
| Phone |
(718) 430-4136
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Cancer center
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (1) |
| GSE19243 |
Genome-wide DNA Methylation Analysis Reveals Novel Targets for Drug Development in Mantle Cell Lymphoma |
|
