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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_3_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 |
pAD3F
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 6 CERAD: C CDR: 0 Gender: male Age: 72 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 |
15068 |
189 |
5676 |
88 |
null |
null |
| 2 |
427 |
147 |
86 |
80 |
null |
null |
| 3 |
3177 |
171 |
6599 |
88 |
-2.45128 |
2.45127914381146 |
| 4 |
685 |
161 |
101 |
87 |
-0.138714 |
0.138714011551571 |
| 5 |
1399 |
180 |
187 |
87 |
-0.634515 |
0.63451540018931 |
| 6 |
1718 |
176 |
151 |
86 |
0.362457 |
-0.362456653783862 |
| 7 |
899 |
172 |
98 |
84 |
0.579892 |
-0.579892279421995 |
| 8 |
843 |
182 |
198 |
86 |
-1.6648 |
1.66480326441273 |
| 9 |
941 |
178 |
102 |
88 |
0.686156 |
-0.686155907155276 |
| 10 |
999 |
184 |
115 |
88 |
0.233264 |
-0.233264418008936 |
| 11 |
392 |
140 |
87 |
84 |
null |
null |
| 12 |
386 |
143 |
86 |
82 |
null |
null |
| 13 |
764 |
165 |
132 |
86 |
-0.898733 |
0.89873251960138 |
| 14 |
823 |
172 |
115 |
88 |
-0.197448 |
0.197447612534951 |
| 15 |
32908 |
196 |
1606 |
85 |
4.31323 |
-4.31322647808557 |
| 16 |
598 |
173 |
98 |
86 |
-0.493793 |
0.493792559426428 |
| 17 |
655 |
169 |
118 |
87 |
-0.89712 |
0.897120377343293 |
| 18 |
6123 |
181 |
131 |
87 |
2.74121 |
-2.74120825490333 |
| 19 |
513 |
171 |
92 |
86 |
-0.558949 |
0.558948578608469 |
| 20 |
5002 |
180 |
173 |
89 |
1.47011 |
-1.47010904629503 |
Total number of rows: 4800
Table truncated, full table size 218 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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