GEO help: Mouse over screen elements for information.
Status
Public on Apr 13, 2009
Title
Lung_normal1_rep2
Sample type
RNA
Channel 1 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 555
Label protocol
Alexa 555 label protocol
Channel 2 Source name
normal lung tissue
Organism
Homo sapiens Characteristics
normal lung tissue
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
349
113
90
77
null
2
388
130
114
78
0.794095763512045
3
339
108
122
77
null
4
377
119
121
80
null
5
366
118
103
76
null
6
364
121
113
77
null
7
349
122
134
81
null
8
424
123
157
81
0.636536094293313
9
371
115
127
79
null
10
379
133
143
78
null
11
395
126
94
79
0.611558036261194
12
391
121
114
78
null
13
1083
130
408
77
2.06824887600226
14
402
126
193
82
null
15
3421
154
289
82
-0.323134686764431
16
721
126
98
80
-1.62304070964364
17
358
122
138
80
null
18
514
139
90
77
-0.320279919747301
19
336
110
109
78
null
20
382
132
107
80
null
4800 150 Kbytes .Supplementary data files not provided Processed data included within Sample table
