|
| Status |
Public on Jul 08, 2009 |
| Title |
miRNA_T00327014_SAMPLE001 |
| Sample type |
other |
| |
|
| Source name |
SCC tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient_id: LS-54
histology: SCC
operation_date: 3-8-99
death: 0
survival_time: 62.4
stage: Ib
t (extent of the primary tumor): 2
n (extent of spread to the lymph nodes ): 0
m (presence of metastasis ): 0
differentiation: mod
age: 76
sex: M
|
| Extracted molecule |
other |
| Extraction protocol |
Total RNA was isolated using Trizol. miRNA was isolated from 4 ug of total RNA using the mirVana isolation kit (Ambion). All samples were then fractionated by polyacrylamide gel electrophoresis (Flash-Page Ambion) and small RNAs (< 40nt) were recovered by ethanol precipitation with linear acrylamide.
|
| Label |
Cy3
|
| Label protocol |
The small RNA samples were subject to poly(A) polymerase reaction wherein amine modified uridines were incorporated (Ambion). The tailed samples were then fluorescently labeled using the amine-reactive Cy3 (Invitrogen). The fluorescently labeled RNAs were purified using a glass-fiber filter and eluted (Ambion).
|
| |
|
| Hybridization protocol |
Each sample was then hybridized to the Bioarray slides for 14 hours at 42oC (Ambion).
|
| Scan protocol |
The arrays were washed and scanned using an Agilent 2505B confocol laser microarray scanner (Agilent) data was obtained using the Expression Analysis software (Codelink, version 4.2)
|
| Description |
no additional information
|
| Data processing |
Probes flagged by the Expression Analysis software were first removed and background median values were subtracted from the spot mean. Spot intensity values below zero were set to 0.5 and the data was then quantile normalized. A background cutoff of 6 (log2 normalized) was identified by plotting the correlations of replicate probes across all samples versus the median of median intensities.
|
| |
|
| Submission date |
May 08, 2009 |
| Last update date |
Jul 08, 2009 |
| Contact name |
Hongtao Fan |
| E-mail(s) |
hfan@cntus.jnj.com
|
| Organization name |
Centocor
|
| Department |
RDI
|
| Street address |
145 King of Prussia Rd
|
| City |
Radnor |
| State/province |
PA |
| ZIP/Postal code |
19087 |
| Country |
USA |
| |
|
| Platform ID |
GPL5106 |
| Series (1) |
| GSE16025 |
miRNA prognostic profiles in lung cancer |
|
