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Sample GSM197693 Query DataSets for GSM197693
Status Public on Oct 15, 2008
Title Carcinoma (F30C_s45_b47)
Sample type genomic
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics disease state: Carcinoma
site: Colorectum
tumor site: Right colon
tnm: pTxN2M0
age: 74
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 CRC23
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 GPL2843
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 1644 263 1819 221 -0.21 0 -0.0767 -0.0767
2 1529.5 275 1660 243 -0.18 0 -0.0767 -0.0767
3 1383 273 1600 242 -0.29 0 -0.0767 -0.0767
4 318 260 326.5 238 -0.61 3
5 320 266 289.5 243 0.22 3
6 300.5 263 276 237 -0.06 2
7 6837 258 6078.5 230 0.17 0 0.0419 0.0419
8 6317 250 5690 220 0.15 0 0.0419 0.0419
9 6580 246 6028 219 0.12 0 0.0419 0.0419
10 360.5 264 321 224 -0.01 0
11 362 259 334 224 -0.09 0
12 357 251 331 218 -0.09 0
13 1268.5 242.5 1252 220 -0.01 0 0.0419 0.0419
14 1061 235 1159 217 -0.19 0 0.0419 0.0419
15 928 234 1087 222.5 -0.32 0 0.0419 0.0419
16 268 228 280 222 -0.54 0
17 279.5 228 291.5 227 -0.32 0
18 308 229 327 229 -0.31 0
19 7913 226 9047.5 231 -0.2 0 0.0419 0.0419
20 7281 225 8616.5 233 -0.25 0 0.0419 0.0419

Total number of rows: 19200

Table truncated, full table size 811 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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