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Sample GSM841203 Query DataSets for GSM841203
Status Public on Apr 01, 2012
Title 2.0N (2006)
Sample type genomic
 
Channel 1
Source name tumors
Organism Homo sapiens
Characteristics disease state: Anal carcinoma
tissue: tumor
Extracted molecule genomic DNA
Extraction protocol DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).
Label Cy5
Label protocol 1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).
 
Channel 2
Source name Reference pooled 46XX
Organism Homo sapiens
Characteristics sample type: Normal female genome
Extracted molecule genomic DNA
Extraction protocol DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).
Label Cy3
Label protocol 1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).
 
 
Hybridization protocol All hybridizations were done for 40 hours at 20 rpm and 65C
Scan protocol Microarray slides were scanned using an Agilent 2565C DNA scanner and images were analyzed with Agilent Feature Extraction version 10.5 using default settings
Data processing The aCGH data from each sorted sample that passed our QC metrics were analyzed in Agilent Genomics Workbench 5.0 using the ADM2 step gram algorithm to identify genomic intervals that were significantly aberrant relative to a normal diploid genome.11 We then ranked the aberrant intervals in each cancer genome based on the relative fold change and the number of annotated genes in each interval.
 
Submission date Nov 30, 2011
Last update date Apr 01, 2012
Contact name Michael Thomas Barrett
E-mail(s) barrett.michael@mayo.edu
Phone 480-301-6736
Organization name Mayo Clinic Arizona
Department Molecular Pharmacology and Experimental Therapeutics
Street address 13400 East Shea Boulevard
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL9777
Series (1)
GSE34063 Clonal Analysis for Identification of Molecular Pathways with Potential Therapeutic Implications in of Rare Gastrointestinal and Endocrine Cancers

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

Data table
ID_REF VALUE
1 1.216309838e-001
2 -2.168868852e-001
3 0.000000000e+000
4 -1.517538607e-001
5 -1.596931014e-001
6 -1.054020376e-001
7 5.555234757e-002
8 2.687514424e-001
9 -5.032217961e-001
10 -1.283516174e-001
11 2.945546769e-001
12 -3.817918503e-002
13 -2.332548041e-002
14 1.061077511e-001
15 2.243436288e-001
16 2.417123875e-001
17 -7.118943125e-002
18 -7.765729777e-002
19 -5.497277640e-001
20 4.002923284e-002

Total number of rows: 420288

Table truncated, full table size 9950 Kbytes.




Supplementary file Size Download File type/resource
GSM841203_US82600137_252185014748_S01_CGH_107_Sep09_1_2.txt.gz 43.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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