NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM197874 Query DataSets for GSM197874
Status Public on Oct 15, 2008
Title Carcinoma component of a progressed adenoma (P2C_s14_b14)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma component of a progressed adenoma
site: Colorectum
tumor site: Rectum
tnm: pTxN0M0
age: 71
gender: F
platform_id type: bac
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 male Reference DNA
Organism Homo sapiens
Characteristics sample type: 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 CRC29
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 05, 2007
Last update date Aug 09, 2010
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 GPL3441
Series (2)
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

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 19755 1711 15514 411 0.26 0 0.3604 0.3604
2 20184 2347.5 15491 466.5 0.25 0 0.3604 0.3604
3 18192 2306.5 15341 465 0.09 0 0.3604 0.3604
4 12385 2336 9807 373 0.09 0 0.0484 0.0484
5 13032 2817.5 9546 439.5 0.17 0 0.0484 0.0484
6 11322 2212 9672 424 -0.02 0 0.0484 0.0484
7 13095 2052 15507 532 -0.44 0 -0.1572 -0.1572
8 12885 1620.5 14828 500.5 -0.35 0 -0.1572 -0.1572
9 13053 2460.5 15109 600 -0.45 0 -0.1572 -0.1572
10 12669 2412.5 10701 538.5 0.01 0 0.0477 0.0477
11 12577 2503 10866 579 -0.03 0 0.0477 0.0477
12 12300 2325 9930 510.5 0.08 0 0.0477 0.0477
13 16906 2248 16119 540.5 -0.09 0 0.088 0.088
14 16190.5 1869.5 16510 509.5 -0.16 0 0.088 0.088
15 15666.5 2705 16273 558.5 -0.28 0 0.088 0.088
16 22179.5 3035.5 16398.5 603 0.28 0 0.3157 0.3157
17 21782.5 2868.5 16606.5 615.5 0.24 0 0.3157 0.3157
18 23041 3251.5 16360.5 633 0.33 0 0.3157 0.3157
19 18095 1343 24958.5 468 -0.55 0 -0.0599 -0.0599
20 17413 1961.5 23487 407.5 -0.58 0 -0.0599 -0.0599

Total number of rows: 15528

Table truncated, full table size 708 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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