 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 11, 2013 |
| Title |
definitive_Alzheimer_7_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 |
dAD7H
|
| Organism |
Homo sapiens |
| Characteristics |
braak: 5 CERAD: C CDR: 2 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 |
13626 |
178 |
4355 |
88 |
null |
null |
| 2 |
361 |
127 |
84 |
83 |
null |
null |
| 3 |
5982 |
155 |
3473 |
86 |
-1.41886 |
1.41886076972768 |
| 4 |
561 |
152 |
107 |
84 |
-0.364665 |
0.364665275188422 |
| 5 |
1213 |
163 |
344 |
85 |
-1.53 |
1.52999632987243 |
| 6 |
1494 |
159 |
136 |
85 |
1.02273 |
-1.02273422737592 |
| 7 |
816 |
148 |
98 |
85 |
1.10584 |
-1.10583582790787 |
| 8 |
760 |
149 |
402 |
85 |
-2.64525 |
2.64524581199712 |
| 9 |
875 |
158 |
99 |
88 |
1.37554 |
-1.37554248289179 |
| 10 |
1105 |
170 |
134 |
86 |
0.575661 |
-0.57566132587915 |
| 11 |
390 |
130 |
84 |
82 |
null |
null |
| 12 |
353 |
125 |
85 |
83 |
null |
null |
| 13 |
566 |
147 |
240 |
84 |
-2.26462 |
2.26461887187737 |
| 14 |
693 |
167 |
108 |
85 |
0.182483 |
-0.182483295675899 |
| 15 |
22742 |
193 |
4051 |
88 |
1.20749 |
-1.20749168341789 |
| 16 |
468 |
144 |
92 |
87 |
-0.00968526 |
0.0096852631820541 |
| 17 |
494 |
141 |
101 |
88 |
-0.320917 |
0.320917305815191 |
| 18 |
5730 |
153 |
287 |
84 |
1.49909 |
-1.49909371427830 |
| 19 |
429 |
141 |
90 |
85 |
-0.299324 |
0.299323769909927 |
| 20 |
5199 |
167 |
332 |
87 |
1.10982 |
-1.1098221769451 |
Total number of rows: 4800
Table truncated, full table size 218 Kbytes.
| Supplementary data files not provided |
| Processed data included within Sample table |
|
|
|
|
 |
