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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_1_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 |
pAD1H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 5 CERAD: C CDR: 0 Gender: female Age: 87 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 |
6057 |
146 |
1347 |
85 |
null |
null |
| 2 |
305 |
102 |
82 |
82 |
null |
null |
| 3 |
3794 |
135 |
2227 |
93 |
-1.43725 |
1.43725080475666 |
| 4 |
503 |
134 |
132 |
90 |
-0.4429 |
0.442899675571387 |
| 5 |
1184 |
137 |
299 |
85 |
-0.482177 |
0.482177328835736 |
| 6 |
1412 |
138 |
163 |
84 |
1.05857 |
-1.05857051577733 |
| 7 |
393 |
117 |
92 |
84 |
-0.079287 |
0.0792869647718355 |
| 8 |
602 |
132 |
422 |
80 |
-2.39759 |
2.39759404018552 |
| 9 |
612 |
118 |
136 |
85 |
-0.107703 |
0.107702573612265 |
| 10 |
1082 |
129 |
157 |
86 |
0.697956 |
-0.697956240734551 |
| 11 |
299 |
100 |
83 |
80 |
null |
null |
| 12 |
298 |
99 |
84 |
82 |
null |
null |
| 13 |
561 |
123 |
133 |
84 |
-0.276784 |
0.276783540750093 |
| 14 |
551 |
135 |
105 |
86 |
0.389302 |
-0.389302010376109 |
| 15 |
23675 |
158 |
1403 |
85 |
2.12413 |
-2.12413383397637 |
| 16 |
407 |
125 |
97 |
84 |
-0.283126 |
0.283125664333834 |
| 17 |
383 |
116 |
98 |
87 |
-0.323558 |
0.323557838621645 |
| 18 |
4258 |
136 |
406 |
84 |
1.13536 |
-1.13536215866741 |
| 19 |
352 |
114 |
89 |
85 |
-0.135112 |
0.135111884454729 |
| 20 |
4261 |
135 |
437 |
85 |
1.03653 |
-1.03652936871903 |
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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