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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_2_frontal_cortex_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
RNA of 15 different 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 |
Cy3
|
| Label protocol |
Protocol Cy3/Cy5
|
| |
|
| Channel 2 |
| Source name |
pAD2F
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 5 CERAD: C CDR: 0 Gender: female Age: 85 years
|
| Extracted molecule |
total RNA |
| Extraction protocol |
kit Pico Pure RNA Isolation Kit
|
| Label |
Cy5
|
| Label protocol |
Protocol Cy3/Cy5
|
| |
|
| |
| 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
|
| Scan protocol |
Hardware: Perkinelmer / Software: ScanArray
|
| 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 |
Lowesss
|
| |
|
| Submission date |
Oct 15, 2008 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Renato David Puga |
| Organization name |
Universidade de São Paulo
|
| Department |
Instituto de Psiquiatria
|
| Lab |
Laboratório de Genética
|
| Street address |
Dr Ovidio Pires de Campos,785
|
| City |
São Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
05403-010 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL1930 |
| Series (1) |
| GSE13214 |
Evaluation of gene expression profile in postmortem brain with Alzheimer´s disease-type neuropathological changes |
|
| 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 |
-[INV_VALUE]: Lowess-normalized log2(Cy3/Cy5) ratios |
| INV_VALUE |
Lowess-normalized log2(Cy3/Cy5) ratios |
| Data table |
| ID_REF |
IntCH1 |
BkgCH1 |
IntCH2 |
BkgCH2 |
VALUE |
INV_VALUE |
| 1 |
1171 |
95 |
323 |
81 |
null |
null |
| 2 |
233 |
77 |
83 |
76 |
null |
null |
| 3 |
2065 |
88 |
1041 |
79 |
-1.71378 |
1.71377672632133 |
| 4 |
283 |
88 |
82 |
75 |
-0.897986 |
0.897985911303802 |
| 5 |
847 |
95 |
166 |
81 |
-0.576217 |
0.576216958032609 |
| 6 |
855 |
93 |
98 |
81 |
0.93656 |
-0.936559994647326 |
| 7 |
272 |
84 |
84 |
80 |
-0.477755 |
0.477754616146032 |
| 8 |
475 |
88 |
131 |
82 |
-1.27372 |
1.27371649772276 |
| 9 |
496 |
86 |
94 |
80 |
-0.133073 |
0.133073421437045 |
| 10 |
833 |
94 |
93 |
82 |
1.21241 |
-1.21240862742292 |
| 11 |
228 |
77 |
80 |
75 |
null |
null |
| 12 |
220 |
76 |
77 |
77 |
null |
null |
| 13 |
383 |
88 |
89 |
81 |
-0.228717 |
0.22871725494445 |
| 14 |
413 |
91 |
86 |
84 |
1.1542 |
-1.1542049020372 |
| 15 |
12183 |
119 |
698 |
79 |
1.89979 |
-1.89979325637146 |
| 16 |
300 |
88 |
86 |
82 |
-0.220894 |
0.220893884432762 |
| 17 |
293 |
88 |
88 |
82 |
-0.645197 |
0.645196818443312 |
| 18 |
3173 |
98 |
203 |
81 |
1.42846 |
-1.42845893171107 |
| 19 |
320 |
90 |
84 |
81 |
0.149906 |
-0.149906161230263 |
| 20 |
2506 |
94 |
151 |
79 |
1.59291 |
-1.59290706770137 |
Total number of rows: 4800
Table truncated, full table size 212 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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