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| Status |
Public on Jan 11, 2013 |
| Title |
pathologic_Alzheimer_2_hippocampus_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
RNA 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 |
pAD2H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 5 CERAD: C CDR: 0 Gender: female Age: 85 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 |
1252 |
130 |
249 |
85 |
null |
null |
| 2 |
265 |
89 |
80 |
81 |
null |
null |
| 3 |
2268 |
108 |
3064 |
85 |
-2.44005 |
2.44005048412050 |
| 4 |
403 |
106 |
107 |
80 |
-0.172399 |
0.172398893833908 |
| 5 |
865 |
121 |
259 |
85 |
-0.36084 |
0.360840154574333 |
| 6 |
1223 |
121 |
289 |
82 |
0.068027 |
-0.0680270276759849 |
| 7 |
360 |
100 |
96 |
84 |
-0.0629408 |
0.0629408098870705 |
| 8 |
453 |
111 |
326 |
81 |
-2.08856 |
2.08855953189075 |
| 9 |
425 |
111 |
123 |
78 |
-0.413523 |
0.413522817352805 |
| 10 |
645 |
108 |
177 |
83 |
-0.231629 |
0.231629143418834 |
| 11 |
269 |
91 |
82 |
79 |
null |
null |
| 12 |
263 |
88 |
82 |
81 |
null |
null |
| 13 |
502 |
109 |
141 |
86 |
-0.135957 |
0.135956573488302 |
| 14 |
434 |
106 |
96 |
82 |
0.42355 |
-0.423550332225772 |
| 15 |
16978 |
136 |
1711 |
82 |
1.60414 |
-1.60414344824384 |
| 16 |
341 |
104 |
92 |
82 |
-0.201173 |
0.201172622473608 |
| 17 |
366 |
110 |
116 |
84 |
-0.614616 |
0.614616402146533 |
| 18 |
3494 |
135 |
372 |
82 |
1.35972 |
-1.35971872365041 |
| 19 |
328 |
103 |
86 |
80 |
-0.0996778 |
0.0996777961692024 |
| 20 |
1963 |
117 |
364 |
82 |
0.457873 |
-0.457873051822398 |
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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