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| Status |
Public on Jan 11, 2013 |
| Title |
definitive_Alzheimer_8_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 |
dAD8H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 4 CERAD: A CDR: 3 Gender: Female Age: 77 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 |
17037 |
173 |
5228 |
86 |
null |
null |
| 2 |
351 |
114 |
87 |
86 |
null |
null |
| 3 |
3963 |
141 |
5993 |
87 |
-2.61952 |
2.61951787199170 |
| 4 |
567 |
132 |
196 |
85 |
-1.27212 |
1.27212359023539 |
| 5 |
1084 |
142 |
338 |
84 |
-1.22786 |
1.22786287797929 |
| 6 |
1709 |
134 |
346 |
85 |
-0.482962 |
0.482962325009052 |
| 7 |
943 |
137 |
103 |
84 |
1.68318 |
-1.68317683919477 |
| 8 |
780 |
146 |
484 |
85 |
-2.4494 |
2.44940051770426 |
| 9 |
882 |
151 |
165 |
86 |
0.0207644 |
-0.0207644077033984 |
| 10 |
1191 |
149 |
437 |
89 |
-1.50837 |
1.50836767083286 |
| 11 |
358 |
123 |
86 |
84 |
null |
null |
| 12 |
339 |
115 |
86 |
85 |
null |
null |
| 13 |
579 |
130 |
164 |
87 |
-0.791526 |
0.791525585837153 |
| 14 |
609 |
133 |
111 |
85 |
0.324703 |
-0.324703022665224 |
| 15 |
29394 |
157 |
2081 |
86 |
2.48735 |
-2.48734688435706 |
| 16 |
458 |
142 |
105 |
87 |
-0.365041 |
0.365041070077543 |
| 17 |
522 |
137 |
254 |
84 |
-1.96803 |
1.96802530230747 |
| 18 |
5889 |
156 |
254 |
84 |
2.23251 |
-2.23250828778408 |
| 19 |
378 |
125 |
91 |
86 |
-0.341464 |
0.34146445857328 |
| 20 |
5512 |
144 |
375 |
86 |
1.45154 |
-1.45153592703319 |
Total number of rows: 4800
Table truncated, full table size 219 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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