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| Status |
Public on Jan 11, 2013 |
| Title |
other_dementias_3_frontal_cortex_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
RNA pool 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 |
OD3F
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 2 CERAD: A CDR: 2 Gender: male Age: 88 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 |
10907 |
155 |
3758 |
85 |
null |
null |
| 2 |
334 |
110 |
85 |
85 |
null |
null |
| 3 |
2723 |
147 |
5361 |
87 |
-2.94201 |
2.94200946149595 |
| 4 |
526 |
140 |
169 |
86 |
-1.00915 |
1.00915141961411 |
| 5 |
1223 |
140 |
437 |
84 |
-1.20176 |
1.20176061414888 |
| 6 |
2145 |
158 |
395 |
85 |
-0.0677584 |
0.0677583560061055 |
| 7 |
677 |
153 |
106 |
85 |
0.860822 |
-0.86082179461282 |
| 8 |
917 |
158 |
198 |
86 |
-0.193235 |
0.193234917745742 |
| 9 |
850 |
159 |
185 |
87 |
-0.189204 |
0.189204435855412 |
| 10 |
1215 |
155 |
141 |
87 |
1.24755 |
-1.247554365931 |
| 11 |
349 |
121 |
85 |
83 |
null |
null |
| 12 |
322 |
110 |
85 |
85 |
null |
null |
| 13 |
622 |
143 |
168 |
87 |
-0.602643 |
0.602643066963902 |
| 14 |
644 |
150 |
143 |
85 |
-0.170929 |
0.170928834712975 |
| 15 |
21462 |
160 |
1937 |
85 |
2.15381 |
-2.15380586240418 |
| 16 |
415 |
128 |
100 |
85 |
-0.385616 |
0.385616173785877 |
| 17 |
542 |
142 |
173 |
85 |
-1.01292 |
1.01291976181294 |
| 18 |
4567 |
168 |
453 |
86 |
1.01415 |
-1.01414636192695 |
| 19 |
438 |
146 |
93 |
89 |
0.235961 |
-0.235961149694068 |
| 20 |
5448 |
159 |
235 |
89 |
2.47204 |
-2.47203983601078 |
Total number of rows: 4800
Table truncated, full table size 220 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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