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Sample GSM318389 Query DataSets for GSM318389
Status Public on Aug 24, 2009
Title Waldenstrom's Macroglobulinemia sample MC93_aCGH
Sample type genomic
 
Channel 1
Source name DNA tumor sample
Organism Homo sapiens
Characteristics Tissue: bone marrow
Age: information unavailable
Gender: Male
Bone marrow involvement: information unavailable
Hemoglobin: information unavailable
B2M: information unavailable
Newly diagnosed: information unavailable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA obtained using standard phenol chloroform extraction method
Label Cy5
Label protocol 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
 
Channel 2
Source name Female reference DNA sample
Organism Homo sapiens
Characteristics reference
Extracted molecule genomic DNA
Extraction protocol Genomic DNA obtained using standard phenol chloroform extraction method
Label Cy3
Label protocol 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
 
 
Hybridization protocol Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.
Scan protocol Scanned on DNA Microarray Scanner (Agilent Technologies).
Images were quantified using Agilent Feature Extraction Software (version 9.5).
Description no additional information
Data processing LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
 
Submission date Sep 05, 2008
Last update date Aug 24, 2009
Contact name Esteban Braggio
E-mail(s) braggio.esteban@mayo.edu
Organization name Mayo Clinic Arizona
Street address 13400 E. Shea Blvd, MCCRB-300
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL4091
Series (1)
GSE12668 Waldenstrom's Macroglobulinemia patients: expression and aCGH data

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
4 0.416377246
5 0.099581689
6 0.044228692
7 0.151144803
8 0.944720984
9 0.257319957
10 -0.590860605
11 0.044647753
12 0.283992618
13 0.060816098
14 0.208020762
15 0.116518572
16 -0.054134101
17 0.022198217
18 4.903285503
19 0.261771291
20 0.167700768
21 0.12167681
22 -0.050390333
23 -0.21296671

Total number of rows: 237834

Table truncated, full table size 4393 Kbytes.




Supplementary file Size Download File type/resource
GSM318389.txt.gz 23.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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