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Status
Public on Apr 13, 2009
Title
Bone_marrow_tumor3_rep1
Sample type
RNA
Channel 1 Source name
bone marrow cancer
Organism
Homo sapiens Characteristics
acute lymphoblastic leukemia
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
274
87
117
81
null
2
307
97
321
81
null
3
270
83
176
78
null
4
286
95
326
82
null
5
310
97
334
82
null
6
295
90
294
81
null
7
292
92
297
82
null
8
324
100
360
82
0.247133097842504
9
293
96
304
80
null
10
322
95
345
79
null
11
297
89
173
80
null
12
295
90
137
80
null
13
951
106
862
82
2.15762469037970
14
436
106
267
82
1.40874765340398
15
655
116
3312
82
-0.327003150477067
16
218
97
536
83
-1.21906125628594
17
290
103
335
80
0.363244315276291
18
572
105
917
82
0.987245330229178
19
294
95
165
81
null
20
336
96
293
80
0.955246994336946
4800 155 Kbytes .Supplementary data files not provided Processed data included within Sample table
