NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM197637 Query DataSets for GSM197637
Status Public on Oct 15, 2008
Title Adenoma component of a progressed adenoma (P24A_s20_b17)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics Adenoma component of a progressed adenoma
Extracted molecule genomic DNA
Extraction protocol as described in Weiss et al, Mol Pathol. 1999 Oct;52(5):243-51.
Label Cy3
Label protocol as described by Snijders et al, Nat Genetics, volume 29, p 263-4
 
Channel 2
Source name female Reference DNA
Organism Homo sapiens
Characteristics A pool of ten normal individuals
Extracted molecule genomic DNA
Extraction protocol DNAzol (Invitrogen) according to manufacturer's protocol
Label Cy5
Label protocol as described by Snijders et al, Nat Genetics, volume 29, p 263-4
 
 
Hybridization protocol as described by Carvalho et al, Cell Oncol. 2006;28(5-6):283-94.
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description n/a
Data processing Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the July 2003 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.
 
Submission date Jun 04, 2007
Last update date Oct 15, 2008
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL3442
Series (1)
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Data table header descriptions
ID_REF
Signal Median CH1 spot signal channel 1 (Cy3)
Background Median CH1 background signal of channel 1 (Cy3)
Signal Median CH2 spot signal channel 2 (Cy5)
Background Median CH2 background signal of channel 1 (Cy5)
Log2ratio
Flag A flag to highlight spots that suffer from poor printing and other experimental artefacts (0 acceptable; 1-4 not acceptable)
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Normalized value of the log2ratio. Flagged features are excluded. Values where also deleted if the each triplicate had a Standard Deviation higher than 0.2.

Data table
ID_REF Signal Median CH1 Background Median CH1 Signal Median CH2 Background Median CH2 Log2ratio Flag VALUE UNF_VALUE
1 10238 121 16998.5 114 -0.74 0
2 14436 84 15970.5 119 -0.14 0
3 10933 78 12960 109 -0.24 0
4 14821 89 20848.5 130 -0.49 0 0.0064 0.0064
5 14706 98 19987 109 -0.44 0 0.0064 0.0064
6 15602 102 20373 114 -0.39 0 0.0064 0.0064
7 8580 88 16511 100 -0.95 0
8 10909.5 88 8333 79 0.39 0
9 12993 71 16034 104 -0.3 0
10 7142 87 9162 100.5 -0.36 0 0.0328 0.0328
11 6766 58 8705.5 108 -0.36 0 0.0328 0.0328
12 7548 71 8771 103 -0.21 0 0.0328 0.0328
13 13273.5 68 15288 97 -0.2 0
14 12679.5 69.5 15184 82 -0.26 0
15 13989 79 15165.5 87.5 -0.12 0
16 9515 113 12123 104 -0.35 0 0.0217 0.0217
17 9385.5 134 12147 102 -0.38 0 0.0217 0.0217
18 9143 134 11766.5 119 -0.37 0 0.0217 0.0217
19 1739 77 1923 99 -0.13 0
20 11130 60 11255 101 -0.01 0

Total number of rows: 15528

Table truncated, full table size 696 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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