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Sample GSM827052 Query DataSets for GSM827052
Status Public on Nov 11, 2011
Title Normal breast tissue Replicate 9
Sample type genomic
 
Channel 1
Source name methylated CpG-island recovery assay (MIRA) enriched, normal breast tissue,non-breast cancer patient 9
Organism Homo sapiens
Characteristics tissue: normal breast
patient: 9
age: 26 years
sample type: methylated
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.
Label cy5
Label protocol The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.
 
Channel 2
Source name input, normal breast tissue,non-breast cancer patient 9
Organism Homo sapiens
Characteristics tissue: normal breast
patient: 9
sample type: Input
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.
Label cy3
Label protocol The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.
 
 
Hybridization protocol According to the instructions of Agilent Oligo aCGH Hybridization Kit
Scan protocol Scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Description Biological replicate 9 of 10,normal breast tissue,non-breast cancer patient
Data processing Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization. Following global mean normalization, probes with an intensity <400 were discarded from further analysis.
 
Submission date Nov 03, 2011
Last update date Jan 20, 2012
Contact name wang liang
E-mail(s) wangliangkexue@163.com
Organization name BioChainBJ
Street address 7A North Yongchang Road BDA
City Beijing
ZIP/Postal code 100176
Country China
 
Platform ID GPL14835
Series (2)
GSE33445 DNA hypermethylation in breast cancer: breast cancer tissues vs. normal breast tissues
GSE33450 DNA hypermethylation and gene expression in breast cancer: breast cancer tissues vs. normal breast tissues

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
PRE_VALUE ratio (Cy5/Cy3) representing test/input

Data table
ID_REF VALUE PRE_VALUE
A_17_P32917065 0.0611 1.043233444
A_17_P32916622 0.3663 1.289042415
A_17_P32912144 -0.1744 0.886146916
A_17_P32905782 0.4953 1.409605905
A_17_P32905555 0.6580 1.577846869
A_17_P32905545 -0.7975 0.575329435
A_17_P32905538 0.8455 1.796843531
A_17_P32905537 0.2097 1.156464078
A_17_P32905432 -0.3239 0.798887114
A_17_P32902315 0.8678 1.824898186
A_17_P32898448 -0.0115 0.992078585
A_17_P32896556 0.0965 1.069190178
A_17_P32889576 0.7661 1.700644622
A_17_P32889537 -0.0809 0.945458738
A_17_P32889532 -1.0907 0.469528199
A_17_P32889528 -1.8816 0.271381251
A_17_P32889238 0.0969 1.069503951
A_17_P32889231 0.4678 1.383030092
A_17_P32889229 -0.1077 0.928058817
A_17_P32888423 0.9211 1.893565502

Total number of rows: 28222

Table truncated, full table size 945 Kbytes.




Supplementary file Size Download File type/resource
GSM827052_US10283824_252984210005_S01_CGH_107_Sep09_1_3.txt.gz 5.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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