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Sample GSM590370 Query DataSets for GSM590370
Status Public on Sep 03, 2010
Title clinical sample 177615
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: 54
sex: M
ipi_stage: 3A
txprimary: CYCL1-CHOP6-RITU
status: With disease, after initial treatment
code_os: ALIVE
code_pfs: ALIVE
overall_survival (years): 1.648186
progression_free_survival (years): 1.648186
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: 54
sex: M
ipi_stage: 3A
txprimary: CYCL1-CHOP6-RITU
status: With disease, after initial treatment
code_os: ALIVE
code_pfs: ALIVE
overall_survival (years): 1.648186
progression_free_survival (years): 1.648186
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: 06-16716
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

Data table header descriptions
ID_REF
VALUE log2 Ratio (HpaII/MspI)

Data table
ID_REF VALUE
MSPI0406S00000183 -0.885422349
MSPI0406S00000238 -1.12501049
MSPI0406S00000239 -0.459630042
MSPI0406S00000300 0.504958987
MSPI0406S00000301 0.546120882
MSPI0406S00000321 0.43570748
MSPI0406S00000352 0.166071624
MSPI0406S00000353 0.032606721
MSPI0406S00000354 0.059129775
MSPI0406S00000360 -0.40817219
MSPI0406S00000361 -0.315965831
MSPI0406S00000384 -0.439458758
MSPI0406S00000385 -0.542425215
MSPI0406S00000410 -0.022605926
MSPI0406S00000433 0.794182181
MSPI0406S00000434 0.374923438
MSPI0406S00000435 0.38181296
MSPI0406S00000479 0.093951762
MSPI0406S00000480 -0.130025834
MSPI0406S00000492 0.484117538

Total number of rows: 25626

Table truncated, full table size 738 Kbytes.




Supplementary file Size Download File type/resource
GSM590370_177615_532.pair.gz 6.2 Mb (ftp)(http) PAIR
GSM590370_177615_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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