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Sample GSM769714 Query DataSets for GSM769714
Status Public on Oct 11, 2011
Title Splenic marginal zone lymphoma BAC_ARRAY_SMZL_03
Sample type genomic
 
Channel 1
Source name DNA SMZL
Organism Homo sapiens
Characteristics tissue: spleen
disease state: Splenic marginal zone lymphomas
Extracted molecule genomic DNA
Extraction protocol The DNA was extracted using the standard phenol-chloroform method. All DNA was quantified using the Nanodrop spectrophotometer (ND-1000, NanoDrop Technologies, Wilmington, DE USA). DNA quality was assessed by the 260:280 ratio and its integrity by agarose gel ethidium bromide visualization.
Label Cy5
Label protocol 2 μg of unamplified genomic DNA (tumour DNA) was digested with DpnII restriction enzyme (New England Biolabs, Beverly, MA) and labelled using random primers (BioPrime Labeling System, Invitrogen, Carlsbad, Calif) and Cy5-dCTP (CyDyeTM 5-dCTP, Amersham Biosciences, Piscataway, NJ) fluorescent dye for paired hybridization samples. The incorporation of labelled nucleotide was quantified using a NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies).
 
Channel 2
Source name Control DNA
Organism Homo sapiens
Characteristics disease state: healthy
sample type: human placenta of healthy donors
tissue: placenta
Extracted molecule genomic DNA
Extraction protocol The DNA was extracted using the standard phenol-chloroform method. All DNA was quantified using the Nanodrop spectrophotometer (ND-1000, NanoDrop Technologies, Wilmington, DE USA). DNA quality was assessed by the 260:280 ratio and its integrity by agarose gel ethidium bromide visualization.
Label Cy3
Label protocol 2 μg of unamplified genomic DNA reference material (placental DNA) was digested with DpnII restriction enzyme (New England Biolabs, Beverly, MA) and labelled using random primers (BioPrime Labeling System, Invitrogen, Carlsbad, Calif) and Cy3-dCTP (CyDyeTM 3-dCTP Amersham Biosciences, Piscataway, NJ) fluorescent dye for paired hybridization samples. The incorporation of labelled nucleotide was quantified using a NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies).
 
 
Hybridization protocol Labelled test and reference DNA samples were mixed equitably, co-precipitated in the presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% formamide, 10% Dextran sulphate, 2X standard saline citrate, 10mM Tris pH 7.6, 2.7% sodium dodecyl sulphate and 10μg/μl of yeast tRNA). DNA mixtures were cohybridized to the arrays in a GENETAC (Genomic Solutions, Ann Arbor, Michigan, USA) for 48 hours at 42ºC in accordance with the manufacturer’s recommended protocol.
Scan protocol Images and signal intensities were acquired using a GenePix 4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePix Pro4.0 (Axon Instruments, Burlingame, CA) imaging software.
Data processing Fluorescence ratios were normalized using the median of the fluorescence ratios of every spot, computed as log2 values. The log2 ratio of each clone was normalized to the median log2 ratio of the 20 control hybridizations, after which the median of the three spots was calculated.
 
Submission date Aug 01, 2011
Last update date Oct 11, 2011
Contact name Cristina Robledo
E-mail(s) crisrmontero@hotmail.com
Organization name CIC
Street address Campus Miguel de Unamuno
City Salamanca
ZIP/Postal code 37007
Country Spain
 
Platform ID GPL13904
Series (1)
GSE31203 Molecular characterization of the chromosome 7 in SMZL

Data table header descriptions
ID_REF
VALUE normalized log2 test/reference

Data table
ID_REF VALUE
1 0.2798
2 0.0215
3 0.0745
4 -0.1779
5 -0.2059
6 -0.1008
7 -0.0072
8 -0.0544
9 -0.0306
10 -0.0014
11 -0.2438
12 -0.0877
13 -0.071
14 -0.1568
15 -0.1329
16 -0.0203
17 -0.125
18 -0.2176
19 -0.1001
20 0.0043

Total number of rows: 3063

Table truncated, full table size 35 Kbytes.




Supplementary file Size Download File type/resource
GSM769714_03_SMZL_BAC_CGH_array.gpr.gz 935.5 Kb (ftp)(http) GPR
Processed data included within Sample table

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