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| Status |
Public on Jan 11, 2013 |
| Title |
definitive_Alzheimer_9_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 |
dAD9H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 6 CERAD: C CDR: 3 Gender: female Age: 83 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 |
17577 |
122 |
5331 |
80 |
null |
null |
| 2 |
308 |
95 |
82 |
83 |
null |
null |
| 3 |
3654 |
122 |
4265 |
85 |
-2.17345 |
2.17345111350912 |
| 4 |
516 |
109 |
122 |
83 |
0.0703689 |
-0.0703688734071086 |
| 5 |
1340 |
131 |
649 |
86 |
-1.35539 |
1.35539301824105 |
| 6 |
1855 |
128 |
352 |
83 |
0.210475 |
-0.210475102649956 |
| 7 |
626 |
121 |
105 |
87 |
1.04168 |
-1.04167534445599 |
| 8 |
737 |
122 |
756 |
84 |
-2.61996 |
2.61995574200407 |
| 9 |
903 |
122 |
181 |
84 |
0.322826 |
-0.322825571360497 |
| 10 |
1083 |
123 |
285 |
83 |
-0.296767 |
0.296766934766195 |
| 11 |
299 |
97 |
84 |
83 |
null |
null |
| 12 |
282 |
97 |
86 |
80 |
null |
null |
| 13 |
665 |
122 |
202 |
85 |
-0.519919 |
0.519919082787431 |
| 14 |
708 |
120 |
152 |
85 |
0.29211 |
-0.292109561875662 |
| 15 |
24140 |
151 |
3500 |
86 |
1.54242 |
-1.54241809616788 |
| 16 |
463 |
115 |
104 |
85 |
0.139518 |
-0.139518315498186 |
| 17 |
495 |
114 |
197 |
84 |
-1.06397 |
1.06396994651674 |
| 18 |
5335 |
124 |
666 |
86 |
0.976307 |
-0.97630666017134 |
| 19 |
400 |
116 |
108 |
87 |
-0.394207 |
0.394207255441332 |
| 20 |
4948 |
126 |
307 |
85 |
2.02966 |
-2.02965881953652 |
Total number of rows: 4800
Table truncated, full table size 220 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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