|
| Status |
Public on Sep 03, 2010 |
| Title |
clinical sample 124424 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DLBCL, MspI representation of genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
molecular_subtypes_by_gene_expression: ABC
pathology: DLBC
site: LN (Lymph Node)
age: 71
sex: F
ipi_stage: 2AE
txprimary: CHOP-RITU
status: LYMPHOMA DEATH
code_os: DEAD
code_pfs: DEAD
overall_survival (years): 0.03285421
progression_free_survival (years): 0.02464066
|
| 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 priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| Channel 2 |
| Source name |
DLBCL, HpaII representation of genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
molecular_subtypes_by_gene_expression: ABC
pathology: DLBC
site: LN (Lymph Node)
age: 71
sex: F
ipi_stage: 2AE
txprimary: CHOP-RITU
status: LYMPHOMA DEATH
code_os: DEAD
code_pfs: DEAD
overall_survival (years): 0.03285421
progression_free_survival (years): 0.02464066
|
| 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 priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| |
| 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 |
Sample name: 99-25549
|
| Data processing |
Raw data (.pair) files generated using NimbleScan software. After QC processing, a median normalization was performed on each array by subtracting the median log-ratio (HpaII/MspI) of that array (resulting in median log-ratio of 0 for each array). SignalMap Version 1.9 software used to generate normalized, log2 ratios. Log2 ratios that were below 2.5MADs of the random probes for each individual array, were considered failed probes and were removed.
|
| |
|
| Submission date |
Sep 03, 2010 |
| Last update date |
Sep 03, 2010 |
| Contact name |
Rita Shaknovich |
| E-mail(s) |
ris9004@med.cornell.edu
|
| Organization name |
Weill Cornell Medical Center
|
| Department |
Medicine
|
| Lab |
Dr.Melnick
|
| Street address |
1300 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (1) |
| GSE23967 |
DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma |
|
