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Status |
Public on Jan 11, 2013 |
Title |
definitive_Alzheimer_3_hippocampus_rep1 |
Sample type |
RNA |
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Channel 1 |
Source name |
dAD3H
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Organism |
Homo sapiens |
Characteristics |
braak: 4 CERAD: C CDR: 1 Gender: female Age: 86 years
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Extracted molecule |
total RNA |
Extraction protocol |
kit Pico Pure RNA Isolation Kit
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Label |
Cy3
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Label protocol |
Protocol Cy3/Cy5
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Channel 2 |
Source name |
Reference RNA
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Organism |
Homo sapiens |
Characteristics |
RNA of 15 different cell lines
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Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00637
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Extracted molecule |
total RNA |
Extraction protocol |
Trizol
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Label |
Cy5
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Label protocol |
Protocol Cy3/Cy5
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Hybridization protocol |
Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao, Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC 2x / Temperature:42 / Time:10 min. / Washing Number: 1 Washing - Round 2 - Solution: SSC 0,1x; SDS 0,1% / Temperature:42 / Time:10 min. / Washing Number: 2 Washing - Round 3 - Solution: SSC 0,1x / Temperature:42 / Time:10 min. / Washing Number: 2
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Scan protocol |
Hardware: Perkinelmer / Software: ScanArray
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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).
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Data processing |
Lowesss
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Submission date |
Oct 15, 2008 |
Last update date |
Jun 12, 2013 |
Contact name |
Renato David Puga |
Organization name |
Universidade de São Paulo
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Department |
Instituto de Psiquiatria
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Lab |
Laboratório de Genética
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Street address |
Dr Ovidio Pires de Campos,785
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City |
São Paulo |
State/province |
São Paulo |
ZIP/Postal code |
05403-010 |
Country |
Brazil |
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Platform ID |
GPL1930 |
Series (1) |
GSE13214 |
Evaluation of gene expression profile in postmortem brain with Alzheimer´s disease-type neuropathological changes |
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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 |
Lowess-normalized log2(Cy3/Cy5) ratios |
Data table |
ID_REF |
IntCH1 |
BkgCH1 |
IntCH2 |
BkgCH2 |
VALUE |
1 |
409 |
102 |
478 |
81 |
null |
2 |
263 |
89 |
82 |
78 |
null |
3 |
3167 |
111 |
923 |
83 |
1.70957071396479 |
4 |
277 |
91 |
98 |
83 |
-0.156741597820243 |
5 |
369 |
104 |
190 |
79 |
0.252781327309626 |
6 |
321 |
104 |
231 |
82 |
-0.342267678032778 |
7 |
275 |
88 |
85 |
83 |
0.110342277297883 |
8 |
363 |
101 |
112 |
81 |
0.630927065505205 |
9 |
278 |
92 |
90 |
81 |
-0.0486843163380462 |
10 |
220 |
99 |
242 |
82 |
-1.88198342661910 |
11 |
253 |
83 |
82 |
80 |
null |
12 |
268 |
87 |
82 |
80 |
null |
13 |
283 |
91 |
93 |
81 |
-0.0311125098722256 |
14 |
288 |
91 |
98 |
83 |
-0.00159961344813730 |
15 |
2035 |
125 |
5828 |
85 |
-2.40961904583298 |
16 |
271 |
89 |
86 |
81 |
0.0102817498114156 |
17 |
274 |
91 |
89 |
80 |
-0.0910925024234537 |
18 |
234 |
108 |
664 |
83 |
-2.21183939488373 |
19 |
247 |
85 |
82 |
81 |
-0.296101663494024 |
20 |
289 |
102 |
422 |
85 |
-0.956509285950263 |
Total number of rows: 4800
Table truncated, full table size 172 Kbytes.
Supplementary data files not provided |
Processed data included within Sample table |
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