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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_4_hippocampus_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| 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 |
Cy3
|
| Label protocol |
Protocol Cy3/Cy5
|
| |
|
| Channel 2 |
| 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 |
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 |
Lowess-normalized log2(Cy3/Cy5) ratios |
| Data table |
| ID_REF |
IntCH1 |
BkgCH1 |
IntCH2 |
BkgCH2 |
VALUE |
| 1 |
15686 |
128 |
7954 |
85 |
null |
| 2 |
276 |
94 |
85 |
84 |
null |
| 3 |
8198 |
113 |
2224 |
87 |
1.73923173384582 |
| 4 |
363 |
112 |
180 |
87 |
-0.000664873365782359 |
| 5 |
865 |
120 |
644 |
84 |
0.849969804819892 |
| 6 |
472 |
123 |
944 |
89 |
-0.895158531220473 |
| 7 |
333 |
108 |
217 |
87 |
-0.423308619517839 |
| 8 |
869 |
125 |
285 |
88 |
2.08922707681621 |
| 9 |
348 |
121 |
408 |
84 |
-0.653553544909353 |
| 10 |
284 |
121 |
498 |
85 |
-1.56343006541777 |
| 11 |
311 |
99 |
85 |
84 |
null |
| 12 |
278 |
94 |
86 |
82 |
null |
| 13 |
462 |
108 |
286 |
84 |
0.64310699978257 |
| 14 |
356 |
107 |
300 |
84 |
-0.294399645245757 |
| 15 |
6368 |
128 |
14311 |
85 |
-2.2482665156991 |
| 16 |
351 |
109 |
162 |
88 |
0.0153204671535634 |
| 17 |
417 |
116 |
170 |
82 |
0.462535424790903 |
| 18 |
548 |
123 |
2296 |
85 |
-1.96365517853122 |
| 19 |
315 |
111 |
95 |
85 |
0.0314849011588922 |
| 20 |
692 |
124 |
2088 |
86 |
-1.42889433336379 |
Total number of rows: 4800
Table truncated, full table size 176 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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