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| Status |
Public on Jan 11, 2013 |
| Title |
definitive_Alzheimer_4_frontal_cortex_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
dAD4F
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 5 CERAD: A CDR: 3 Gender: female Age: 83 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 |
521 |
119 |
382 |
87 |
null |
| 2 |
276 |
91 |
89 |
85 |
null |
| 3 |
3507 |
136 |
997 |
91 |
2.68677690856293 |
| 4 |
314 |
104 |
150 |
87 |
0.368856754788646 |
| 5 |
505 |
111 |
518 |
89 |
0.959416490731658 |
| 6 |
232 |
104 |
622 |
91 |
-1.30140634339521 |
| 7 |
416 |
98 |
1351 |
88 |
null |
| 8 |
933 |
119 |
281 |
88 |
3.14697028940431 |
| 9 |
357 |
109 |
218 |
93 |
0.977976986992398 |
| 10 |
367 |
118 |
514 |
86 |
0.171584809199238 |
| 11 |
289 |
95 |
87 |
85 |
null |
| 12 |
275 |
93 |
89 |
86 |
null |
| 13 |
341 |
106 |
157 |
87 |
0.669778913543824 |
| 14 |
322 |
101 |
259 |
89 |
0.694350562187423 |
| 15 |
899 |
123 |
7725 |
94 |
-2.78429237095395 |
| 16 |
322 |
106 |
139 |
90 |
0.490086743274296 |
| 17 |
296 |
100 |
135 |
89 |
0.237819822184972 |
| 18 |
361 |
118 |
1783 |
90 |
-1.52453160266704 |
| 19 |
323 |
105 |
125 |
88 |
0.562579511461767 |
| 20 |
267 |
115 |
1070 |
86 |
-1.63583424232455 |
Total number of rows: 4800
Table truncated, full table size 174 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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