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Sample GSM198829 Query DataSets for GSM198829
Status Public on Oct 15, 2008
Title Adenoma (F48A_expr_s85_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 2280 466 475 204 2.74 0 1.688217555 1.688217555
2 1914.5 787 476 250 2.32 1 1.254204472
3 25099 707 2862 257 3.23 1 1.116758987
4 609 478 293 190 0.35 2 -1.043599856
5 780 352 370 170 1.1 0 -0.027805335 -0.027805335
6 33446 3704.5 4514 461 2.88 1 0.529416799
7 23705 1817 3156 271 2.92 1 0.815422334
8 6715.5 1049 642 213 3.72 1 2.6338094
9 1473 402 668.5 141 1.02 1 -0.031818295
10 5844.5 317 1238.5 123 2.31 0 1.02742611 1.02742611
11 1063.5 258 920 119 0.01 0 -1.04311292 -1.04311292
12 1843 232 316 116 3.01 0 1.955512956 1.955512956
13 535 218 207.5 116 1.79 0 0.497130754 0.497130754
14 427 203.5 982.5 114 -1.96 0 -3.032307864 -3.032307864
15 2053.5 201.5 881.5 115.5 1.27 0 0.211827574 0.211827574
16 1273 192 901.5 117 0.46 0 -0.582378407 -0.582378407
17 2701 180.5 1001 115 1.51 0 0.423245559 0.423245559
18 1174 175 1123 116 -0.01 0 -1.05716517 -1.05716517
19 1165.5 172 532 116 1.26 0 0.203566557 0.203566557
20 1397 169 726 116 1.01 0 -0.037406205 -0.037406205

Total number of rows: 30000

Table truncated, full table size 1532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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