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Sample GSM1370600 Query DataSets for GSM1370600
Status Public on Apr 18, 2014
Title case 1
Sample type genomic
 
Channel 1
Source name transformed DLBCL (GC)
Organism Homo sapiens
Characteristics tissue: transformed DLBCL (GC)
gender: male
age: 86
Extracted molecule genomic DNA
Extraction protocol Proteinase K digestion followed by phenol_chloroform extraction
Label Cy5
Label protocol 400 ng of tumor and reference genomic DNA was labeled with Cy5dCTP or Cy3dCTP (Amersham Biosciences, Little Chalfont, UK) respectively using a BioPrime Kit (Invitrogen, Palsely, UK) with custom-made dNTP mix (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM).
 
Channel 2
Source name Mixed normal blood from 20 individuals (reference)
Organism Homo sapiens
Characteristics gender: female
tissue: blood
Extracted molecule genomic DNA
Extraction protocol Proteinase K digestion followed by phenol_chloroform extraction
Label Cy3
Label protocol 400 ng of tumor and reference genomic DNA was labeled with Cy5dCTP or Cy3dCTP (Amersham Biosciences, Little Chalfont, UK) respectively using a BioPrime Kit (Invitrogen, Palsely, UK) with custom-made dNTP mix (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM).
 
 
Hybridization protocol The purified DNA from test and reference were pooled and mixed with 45μg of Cot1 DNA and 200 μg of Herring sperm DNA and precipitated. The precipitated DNA was dissolved in 30 μl hybridisation buffer, incubated at 37°C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37°C for 48 hours under a coverslip. The arrays then washed successively in 1xPBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42°C for 30 min once, 1 x PBS/0.05% Tween 20 at room temperature for 15 min and 1 x PBS for 5 min twice. Dried by centrifugation.
Scan protocol Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.
Data processing The median of the ratio of test reference spot intensity, after subtraction of local background was used as the normalization factor. The chromosomal arm on which the most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was devided by normalization factor of each subarray, an avarage of the duplicate calculated and log2-transformed.
 
Submission date Apr 17, 2014
Last update date Apr 18, 2014
Contact name Anna Kwiecinska
E-mail(s) anna.kwiecinska@ki.se
Organization name Karolinska Institute
Department Oncology-Pathology
Street address CCK R8:00
City Stockholm
ZIP/Postal code 17176
Country Sweden
 
Platform ID GPL18586
Series (1)
GSE56884 Array based comparative genomic hybridisation analysis of 1 Mb resolution of 21 follicular lymphomas (FL), 31 transformed diffuse large B-cells lymphomas (DLBCL), 29 de novo DLBCL (10 of GC and 19 non-GC related immunophenotype).

Data table header descriptions
ID_REF
VALUE log2 Cy5/Cy3 representing tumor/reference intensity ratio for analysis of copy number variation

Data table
ID_REF VALUE
1 -0.242433991
2 -0.778276567
3 -0.659557891
4 -0.990256666
5 -0.411388863
6 -0.540791641
7 0.422802623
8 0.500465853
9 0.250835109
10 0.256528443
11 0.094031186
12 -0.081639901
13 -0.105858229
14 -0.247487591
15 -0.226292663
16 -0.342774886
17 -0.081767807
18 -0.198849209
19 -0.663823144
20 -0.240586169

Total number of rows: 3038

Table truncated, full table size 49 Kbytes.




Supplementary file Size Download File type/resource
GSM1370600_1Mb_1441_slide36_A1-1.gpr.gz 764.9 Kb (ftp)(http) GPR
GSM1370600_case_1_1Mb_Plots4x4V6_Batch1441_Slide65_Array1.xls.gz 973.9 Kb (ftp)(http) XLS
Processed data included within Sample table
Processed data provided as supplementary file

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