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Sample GSM198816 Query DataSets for GSM198816
Status Public on Oct 15, 2008
Title Adenoma (F37A_expr_s82_b34)
Sample type RNA
 
Channel 1
Source name colon
Organism Homo sapiens
Characteristics Adenoma
Extracted molecule total RNA
Extraction protocol protocol available on wwww.vumc.nl/microarrays/
Label Cy3
Label protocol As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47.
 
Channel 2
Source name universal human reference RNA, Stratagene
Organism Homo sapiens
Characteristics comprised of 10 cell lines for human giving broad gene coverage
Extracted molecule total RNA
Extraction protocol See www.stratagene.com
Label Cy5
Label protocol As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47
 
 
Hybridization protocol As described in Muris et al, Br J Haematol. 2007 Jan;136(1):38-47
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, as described in Carvalho et al, submitted
 
Submission date Jun 07, 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 GPL3055
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 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
1 627 578 279 269 2.29 2 0.813777762
2 822 680.5 367.5 298 1.03 1 -0.301004875
3 3293 970 4283 218 -0.81 1 -1.728621699
4 2783 781 737 153 1.78 0 0.672622548 0.672622548
5 4289 533.5 982 137.5 2.15 0 1.126072744 1.126072744
6 606 370 177.5 122 2.09 0 0.787645553 0.787645553
7 631.5 328 286 119 0.86 0 -0.364594082 -0.364594082
8 2895 294 906 116 1.72 0 0.649477061 0.649477061
9 1141 297 925 117 0.06 0 -1.047984865 -1.047984865
10 2230 299 1025.5 118 1.09 0 0.006515604 0.006515604
11 754 296 751 117 -0.47 0 -1.583429586 -1.583429586
12 1084 300 240 116 2.66 0 1.513602337 1.513602337
13 691 293.5 188 116 2.46 0 1.190358227 1.190358227
14 465 290 1405.5 117 -2.88 0 -3.99734775 -3.99734775
15 2426 265 912.5 114 1.44 3 0.352292395
16 682 252 862.5 117.5 -0.79 0 -1.905159811 -1.905159811
17 3043.5 252 1072 118 1.55 0 0.50317985 0.50317985
18 1622 228 1449 115 0.06 0 -1.014830239 -1.014830239
19 1439 224 567 114 1.42 0 0.314718293 0.314718293
20 1760 222.5 777 115 1.22 0 0.106957597 0.106957597

Total number of rows: 30000

Table truncated, full table size 1555 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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