NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM197695 Query DataSets for GSM197695
Status Public on Oct 15, 2008
Title Carcinoma (F32C_s48_b16)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma
site: Colorectum
tumor site: Right colon
tnm: pT3N0M0
age: 65
gender: F
platform_id type: bac
Extracted molecule genomic DNA
Extraction protocol protocol available on www.vumc.nl/microarrays
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 CRC16
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 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 GPL3442
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 frmo poor prinitng 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 4222.5 687 4265.5 122 -0.23 0
2 4454 714 4395 122 -0.19 0
3 4511.5 713 4576 126 -0.23 0
4 5681 668.5 5310.5 129 -0.05 0 -0.0033 -0.0033
5 5585 584 5362 129 -0.07 0 -0.0033 -0.0033
6 5441.5 562.5 5095 128 -0.03 0 -0.0033 -0.0033
7 4073 507 4639 125 -0.34 0
8 4082 475 4620.5 122 -0.32 0
9 4276 560 4406 124 -0.2 0
10 2662.5 509 2612 125 -0.21 0 -0.0425 -0.0425
11 2654 586 2598.5 124 -0.26 0 -0.0425 -0.0425
12 2834.5 647.5 2488.5 125 -0.11 0 -0.0425 -0.0425
13 4472 581 4775.5 122 -0.26 0
14 4722 599 5102 126 -0.27 0
15 4640 568 5297 124 -0.35 0
16 3834 581 3494 124 -0.05 0 0.0329 0.0329
17 3706 560 3584 126 -0.14 0 0.0329 0.0329
18 3399 424 3352.5 127 -0.12 0 0.0329 0.0329
19 3995.5 603.5 4204.5 124 -0.27 0
20 3879.5 633.5 4132 122 -0.3 0

Total number of rows: 15528

Table truncated, full table size 662 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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