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| Status |
Public on Jan 11, 2013 |
| Title |
normal_brain_10_hippocampus_rep2 |
| Sample type |
RNA |
| |
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| 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 |
N10H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 2 CERAD: 0 CDR: 0 Gender: female Age: 94 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
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| 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 |
1148 |
184 |
293 |
98 |
null |
null |
| 2 |
433 |
155 |
96 |
97 |
null |
null |
| 3 |
648 |
180 |
644 |
92 |
-2.6365 |
2.63649812761566 |
| 4 |
461 |
161 |
101 |
91 |
-0.15762 |
0.157620144722956 |
| 5 |
544 |
178 |
114 |
90 |
-0.0359655 |
0.0359654970073673 |
| 6 |
555 |
187 |
110 |
92 |
0.114518 |
-0.114518192127687 |
| 7 |
497 |
162 |
103 |
92 |
0.0825982 |
-0.0825982395757414 |
| 8 |
467 |
165 |
109 |
97 |
-0.20993 |
0.209930199856685 |
| 9 |
499 |
172 |
94 |
94 |
null |
null |
| 10 |
503 |
175 |
100 |
97 |
0.379696 |
-0.379696176742232 |
| 11 |
432 |
148 |
101 |
93 |
null |
null |
| 12 |
453 |
157 |
103 |
93 |
null |
null |
| 13 |
469 |
155 |
93 |
97 |
null |
null |
| 14 |
482 |
174 |
92 |
91 |
0.422123 |
-0.422123465003159 |
| 15 |
5363 |
203 |
457 |
94 |
1.59316 |
-1.59316424769034 |
| 16 |
470 |
165 |
93 |
93 |
null |
null |
| 17 |
453 |
151 |
100 |
90 |
-0.14074 |
0.140739514044264 |
| 18 |
1031 |
177 |
155 |
91 |
0.815719 |
-0.815719382395857 |
| 19 |
439 |
150 |
97 |
90 |
-0.144329 |
0.144329153007186 |
| 20 |
921 |
200 |
143 |
96 |
0.862436 |
-0.86243554886187 |
Total number of rows: 4800
Table truncated, full table size 217 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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