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| Status |
Public on Jan 11, 2013 |
| Title |
normal_brain_9_frontal_cortex_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 |
N9F
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 0 CERAD: 0 CDR: 0 Gender: female Age: 82 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 |
12706 |
141 |
3927 |
88 |
null |
null |
| 2 |
299 |
105 |
86 |
84 |
null |
null |
| 3 |
3579 |
138 |
2234 |
88 |
-2.08494 |
2.08493972707316 |
| 4 |
471 |
123 |
95 |
89 |
0.00462967 |
-0.00462967116758861 |
| 5 |
1185 |
132 |
232 |
89 |
-1.05736 |
1.05735741584604 |
| 6 |
1642 |
141 |
128 |
87 |
1.19858 |
-1.19857788511305 |
| 7 |
562 |
131 |
92 |
88 |
0.746301 |
-0.746301482442822 |
| 8 |
856 |
149 |
466 |
91 |
-2.90905 |
2.90905028424067 |
| 9 |
789 |
147 |
97 |
89 |
0.986817 |
-0.986816978385167 |
| 10 |
1013 |
151 |
116 |
90 |
0.605036 |
-0.605035615268636 |
| 11 |
321 |
110 |
86 |
82 |
null |
null |
| 12 |
300 |
100 |
86 |
86 |
null |
null |
| 13 |
635 |
119 |
145 |
87 |
-1.13508 |
1.13507794046802 |
| 14 |
587 |
125 |
95 |
86 |
0.241287 |
-0.241286972076127 |
| 15 |
20298 |
147 |
937 |
90 |
2.35891 |
-2.35891417527863 |
| 16 |
406 |
125 |
94 |
89 |
-0.377581 |
0.377580951238029 |
| 17 |
462 |
133 |
107 |
88 |
-1.12812 |
1.12811502270618 |
| 18 |
4171 |
154 |
139 |
89 |
2.43544 |
-2.43543612486827 |
| 19 |
371 |
126 |
90 |
89 |
-0.18439 |
0.184389559303898 |
| 20 |
3776 |
149 |
270 |
90 |
0.677967 |
-0.67796731487657 |
Total number of rows: 4800
Table truncated, full table size 216 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
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