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Status
Public on Apr 13, 2009
Title
Head_neck_normal1_rep1
Sample type
RNA
Channel 1 Source name
normal head & neck tissue
Organism
Homo sapiens Characteristics
normal head & neck tissue - palate_maxilla
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
362
117
94
79
null
2
518
131
246
82
0.335066915677765
3
324
109
98
77
null
4
468
131
270
82
-0.0627450298883624
5
489
141
334
83
-0.204459129852849
6
652
140
269
81
0.83389555511134
7
523
145
306
81
0.0546702975079504
8
788
152
304
84
1.07827255115521
9
431
138
157
81
-0.126387211066285
10
490
149
203
83
0.224435177438289
11
379
121
107
80
null
12
458
142
185
82
0.0643109724282329
13
2525
152
1083
80
2.27908931171317
14
481
141
338
84
-0.262689972369955
15
2191
161
7683
86
-0.729816333569616
16
613
137
1160
81
-0.821927876649966
17
488
140
230
81
0.173467777023627
18
1546
151
1336
84
1.10478657558478
19
415
138
171
84
null
20
614
157
247
84
0.701921323763722
4800 174 Kbytes .Supplementary data files not provided Processed data included within Sample table
