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Sample GSM849824 Query DataSets for GSM849824
Status Public on Dec 20, 2011
Title Human Rectal Adenoma Replicate 4
Sample type genomic
 
Channel 1
Source name Human Rectal Adenoma Biopsy Tissue
Organism Homo sapiens
Characteristics tissue: Adenoma
age: 47
Sex: Male
location: Rectal
Treatment protocol Biopsy tissue was obtained by colonoscopy and stored at -80 ℃ until DNA extraction.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
Label cy3
Label protocol 500 ng the reference commercial genomic DNA (promega) and the same amount of adenoma/carcinoma DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
 
Channel 2
Source name Commercial Human Genomic DNA: Male
Organism Homo sapiens
Characteristics company: Promega
catalog: G1471
Treatment protocol Biopsy tissue was obtained by colonoscopy and stored at -80 ℃ until DNA extraction.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
Label cy5
Label protocol 500 ng the reference commercial genomic DNA (promega) and the same amount of adenoma/carcinoma DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
 
 
Hybridization protocol Reference DNA probes and adenoma/carcinoma DNA probes was combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.
Scan protocol Scanned on an Agilent G2565BA Scanner
Description Biological replicate 4 of 8.Human Rectal Adenoma Biopsy Tissue
Data processing Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Agilent Genomic Workbench Lite Edition 6.5 was used to normalize and analyze the probe data.
 
Submission date Dec 15, 2011
Last update date Dec 20, 2011
Contact name Ming-Rong Wang
E-mail(s) wangmr2015@cicams.ac.cn
Organization name Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
Street address 17 Panjiayuan Nanli, Chaoyang District, Beijing, China
City Beijing
ZIP/Postal code 100021
Country China
 
Platform ID GPL8841
Series (1)
GSE34472 Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases)

Data table header descriptions
ID_REF
VALUE Agilent Genomic Workbench Lite Edition 6.5 normalized ratio test/ref (ch1/ch2)

Data table
ID_REF VALUE
A_14_P112718 0.6871167
A_14_P201353 -0.3560085
A_14_P108353 0.009760673
A_14_P129881 0.207113
A_14_P114030 0.40329203
A_14_P139527 0.36178514
A_14_P118340 0.64956504
A_14_P106890 0.0747463
A_14_P122641 -0.43334648
A_14_P107170 0.24177165
A_14_P100766 0.07964778
A_14_P118104 -0.08314465
A_14_P117253 0.5344076
A_14_P129407 0.33037695
A_14_P200001 0.29943958
A_14_P103811 0.10706292
A_14_P119666 0.6844796
A_14_P100799 -0.022950878
A_14_P121179 0.23159242
A_14_P115318 0.34787545

Total number of rows: 42254

Table truncated, full table size 1007 Kbytes.




Supplementary file Size Download File type/resource
GSM849824.txt.gz 13.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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