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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_4_hippocampus_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 |
pAD4H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 6 CERAD: C CDR: 3 Gender: female Age: 86 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 |
16714 |
139 |
5552 |
85 |
null |
null |
| 2 |
347 |
109 |
84 |
84 |
null |
null |
| 3 |
5608 |
141 |
2460 |
85 |
-1.58655 |
1.58654741629561 |
| 4 |
587 |
123 |
103 |
85 |
-0.166107 |
0.166107045222905 |
| 5 |
1582 |
137 |
284 |
83 |
-0.999027 |
0.99902688842591 |
| 6 |
2002 |
125 |
141 |
84 |
1.12528 |
-1.12527692238409 |
| 7 |
660 |
117 |
90 |
85 |
1.14377 |
-1.1437727768889 |
| 8 |
862 |
121 |
272 |
83 |
-1.9237 |
1.92370034819052 |
| 9 |
918 |
120 |
97 |
83 |
1.13492 |
-1.13492099203107 |
| 10 |
1274 |
126 |
102 |
83 |
1.54277 |
-1.54276879447372 |
| 11 |
330 |
110 |
82 |
81 |
null |
null |
| 12 |
392 |
109 |
86 |
83 |
null |
null |
| 13 |
1370 |
125 |
282 |
86 |
null |
null |
| 14 |
683 |
131 |
98 |
85 |
0.467777 |
-0.467776960811539 |
| 15 |
26716 |
149 |
2125 |
82 |
1.85491 |
-1.85490896758254 |
| 16 |
442 |
119 |
90 |
84 |
-0.142069 |
0.142068571874829 |
| 17 |
543 |
118 |
131 |
83 |
-1.26621 |
1.26621192161098 |
| 18 |
5736 |
145 |
233 |
85 |
1.55417 |
-1.55417074991338 |
| 19 |
397 |
119 |
90 |
85 |
-0.374691 |
0.3746910951255 |
| 20 |
5990 |
130 |
258 |
85 |
1.44882 |
-1.44882454022355 |
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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