NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1082764 Query DataSets for GSM1082764
Status Public on Feb 14, 2013
Title Normal colon tissue, NBRCCC003
Sample type genomic
 
Channel 1
Source name Normal colon tissue, recurrence-free group
Organism Homo sapiens
Characteristics tissue: normal colon adjacent to colon cancer
age: 52 yr
relapse status: recurrence-free
Growth protocol Tissues were obtained and immediately snap-frozen in liquid nitrogen and stored.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was prepared using the phenol/chloroform/isoamyl alcohol method.
Label Cy5
Label protocol Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.
 
Channel 2
Source name Commerical gDNA
Organism Homo sapiens
Characteristics sample type: reference
Extracted molecule genomic DNA
Extraction protocol Control DNA: Promega #G1471 (male) and #G1521 (female).
Label Cy3
Label protocol Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.
 
 
Hybridization protocol The labeled DNA was denatured and pre-annealed with Cot-1 DNA and Agilent blocking reagent and hybridized for 40 hours at 20 rpm in an Agilent hybridization oven.
Scan protocol The arrays were scanned at 5-㎛ resolution using an Agilent scanner (Agilent), and the image was analyzed with Feature Extraction Software 9.1.1.1.
Images were quantified using Agilent Feature Extraction Software.
Description NBRCCC003
Data processing Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
 
Submission date Feb 13, 2013
Last update date Feb 14, 2013
Contact name Park Chan Hee
E-mail(s) haema@yuhs.ac
Phone 80222277650
Organization name Cancer Metastasis Research Center
Street address Shinchondong 134
City Seodaemun-gu
State/province Seoul
ZIP/Postal code 120-752
Country South Korea
 
Platform ID GPL8841
Series (1)
GSE44300 DNA profiling of human normal colon tissues

Data table header descriptions
ID_REF
VALUE Normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_14_P100000 -0.331585526
A_14_P100001 0.267750204
A_14_P100002 -0.687992394
A_14_P100003 -1.137225509
A_14_P100004 1.006910205
A_14_P100005 0.084691174
A_14_P100006 0.343864352
A_14_P100007 -0.018121038
A_14_P100008 -0.81062454
A_14_P100009 0.111315064
A_14_P100010 0.388909459
A_14_P100011 0.472802609
A_14_P100012 -0.385283649
A_14_P100013 0.340731353
A_14_P100014 -0.571262479
A_14_P100015 0.598304152
A_14_P100016 -0.001772121
A_14_P100017 0.311979622
A_14_P100018 -0.213188633
A_14_P100019 0.050761417

Total number of rows: 42424

Table truncated, full table size 1052 Kbytes.




Supplementary file Size Download File type/resource
GSM1082764_NBRCCC003.txt.gz 14.0 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap