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Sample GSM1024662 Query DataSets for GSM1024662
Status Public on Oct 25, 2012
Title T212
Sample type genomic
 
Channel 1
Source name Peripheral blood
Organism Homo sapiens
Characteristics tissue: peripheral blood
Extracted molecule genomic DNA
Extraction protocol Normal blood DNA was extracted with the QIAGEN Flexigene Kit (Cat No.: 51206).
Label Cy3
Label protocol 500ng sample and normal genomic DNA were fragmented by restriction digestion with Alu I/Rsa I (65degrees C for 20mins) and then were labeled with Cy5 and Cy3, respectively, at 85C for 30 min. Labeled DNA were purified using Microcon 30kDa spin columns. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nm(Cy5) using a NanoDrop.
 
Channel 2
Source name Colorectal tumor tissue
Organism Homo sapiens
Characteristics tissue: colorectal tumor
Extracted molecule genomic DNA
Extraction protocol Tumor DNA was extracted from fresh frozen material using the QIAGEN Blood & Cell Culture DNA Maxi Kit (Cat. No.: 13362).
Label Cy5
Label protocol 500ng sample and normal genomic DNA were fragmented by restriction digestion with Alu I/Rsa I (65degrees C for 20mins) and then were labeled with Cy5 and Cy3, respectively, at 85C for 30 min. Labeled DNA were purified using Microcon 30kDa spin columns. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nm(Cy5) using a NanoDrop.
 
 
Hybridization protocol Appropriate equal amounts of Cy5-labeled sample and Cy3-labeled reference DNA were mixed to a 39ul final volume. 71ul Hybridization Master Mix (1mg/ml Cot-1 DNA 5ul, Agilent 10X blocking agent 11ul, and Agilent 2X HiRPM Hybridization buffer 55ul) was added and incubated at 95C for 3 min followed by 37C for 30min. 100ul of the hybridization sample mixture was applied onto the microarray gasket well and was covered by a microarray slide. The slide was incubated in a 65C rotator rack for 24 hours. After hybridization, slide was washed sequentially.
Scan protocol Scanned on Agilent Technologies Scanner G2505C US83603551. Images were quantified using Agilent Feature Extraction Software (v10.7.3.1).
Data processing Agilent Feature Extraction Software (v10.7.3.1) was used for background subtraction and Lowess normalization.
 
Submission date Oct 24, 2012
Last update date Oct 25, 2012
Contact name Ian Wallace Brock
E-mail(s) i.w.brock@sheffield.ac.uk
Phone 01142713165
Fax 447950304013
Organization name University of Sheffield Medical School
Department Cancer Studies
Lab Cox
Street address Beachhill Road
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2RX
Country United Kingdom
 
Platform ID GPL10123
Series (1)
GSE41813 Colorectal tumor DNA vs. normal control DNA

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 8.291572858e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
14 0.000000000e+000
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4213 Kbytes.




Supplementary file Size Download File type/resource
GSM1024662_US83603551_252206018358_S01_CGH_107_Sep09_1_4.txt.gz 18.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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