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Status
Public on Apr 13, 2009
Title
Stomach_tumor1_rep1
Sample type
RNA
Channel 1 Source name
stomach cancer
Organism
Homo sapiens Characteristics
gastrointestinal stromal stomach carcinoma
Extracted molecule
total RNA
Extraction protocol
Trizol
Label
Alexa 555
Label protocol
Alexa 555 label protocol
Channel 2 Source name
reference RNA pool
Organism
Homo sapiens Characteristics
RNA pool of 15 distinct cell lines
Biomaterial provider
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00637
Extracted molecule
total RNA
Extraction protocol
Trizol
Label
Alexa 647
Label protocol
Alexa 647 label protocol
Hybridization protocol
Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deionized formamide 40% / Temperature:42 / Time:12-24h / Touch Down: 70, 55, 50, 42
Scan protocol
Slides were scanned on a confocal laser scanner (ScannArray Express, Perkin Elmer), using identical parameters for all slides and data was extracted with ScanArray Express software (Perkin Elmer). Glass Slides were scanned at different photomultiplier tube (pmt) gains, being 70% and 60% for the channels 1 (Alexa Fluor 555) and 2 (Alexa Fluor 647), respectively.
Description
Reference RNA: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU 145 (prostate carcinoma), FaDu (pharinx squamous cell carcinoma), GM-637 (fibroblast), H-146 (small cell lung carcinoma), HT-1080 (fibrosarcoma), HB4a (normal mammary luminal epithelium), HEK (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma), T98G (glioblastoma multiforme).
Data processing
After subtracting local background, data was normalized by Lowess (R Project) and dye swaps were reversed during normalization.
Submission date
Sep 10, 2008
Last update date
May 13, 2009
Contact name
Barbara Pereira Mello
E-mail(s)
bmello@lbhc.hcancer.org.br Phone
55-11-2189-5000-1134
Organization name
Hospital A. C. Camargo
Department
Centro de Pesquisa
Lab
LBHC
Street address
R. Prof. Antonio Prudente, 211
City
Sao Paulo
State/province
SP
ZIP/Postal code
01509-900
Country
Brazil
Platform ID
GPL7262 Series (1)
GSE12737 No-match ORESTES explored as tumor markers
Data table header descriptions ID_REF this column should correspond to the ID column of the reference platform
IntCH1 Channel 1 Intensity
BkgCH1 BackGround Channel 1
IntCH2 Channel 2 Intensity
BkgCH2 BackGround Channel 2
VALUE value normalized by Lowess representing test/reference RNA pool
Data table ID_REF IntCH1 BkgCH1 IntCH2 BkgCH2 VALUE 1
355
117
104
80
null
2
405
127
293
82
null
3
330
106
100
77
null
4
383
130
323
79
-0.0334790134532617
5
355
143
492
79
-0.483262050107733
6
362
127
390
82
-0.0812586586544048
7
421
139
241
82
-0.0325784475022309
8
427
139
280
81
0.250306753651968
9
369
123
109
82
null
10
353
119
160
83
null
11
380
128
124
77
null
12
378
124
141
77
null
13
1447
151
765
82
2.45594229573070
14
393
128
403
80
0.192379340419843
15
1247
154
6780
88
-0.435963190580665
16
337
125
460
83
null
17
395
132
338
81
0.176624920465581
18
726
153
719
81
0.593659675989219
19
372
126
105
77
null
20
594
157
149
81
1.04851200953994
4800 168 Kbytes .Supplementary data files not provided Processed data included within Sample table
