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Status
Public on Apr 13, 2009
Title
Breast_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 breast tissue
Organism
Homo sapiens Characteristics
normal breast 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
338
109
88
76
null
2
453
129
180
80
-0.0892620512253512
3
322
105
107
77
null
4
417
128
117
81
-0.0871354269465021
5
447
138
267
82
0.464662581010376
6
438
127
210
83
0.158896633186183
7
397
125
225
79
0.549317184866856
8
425
130
181
78
0.144583653322293
9
367
125
126
82
null
10
395
132
182
80
null
11
371
118
111
76
null
12
402
125
199
79
0.378284098901681
13
1068
138
1086
81
2.63081823104710
14
390
127
159
81
0.334386537345618
15
11478
153
1034
83
-1.06903546421547
16
542
139
129
77
-0.891204711040765
17
393
130
185
80
null
18
1040
149
385
80
-0.00107060858083052
19
358
114
120
84
null
20
391
127
211
81
null
4800 169 Kbytes .Supplementary data files not provided Processed data included within Sample table
