|
| Status |
Public on Dec 01, 2009 |
| Title |
251485028602_4 |
| Sample type |
RNA |
| |
|
| Source name |
ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
control_RNAi
24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIZOL reagent (Invitrogen) followed by RNeasy mini kit with DNase on-column digestion (Qiagen). RNA was quantified with NanoDrop ND-1000 followed by quality assessment with the 2100 Bioanalyzer (Agilent) according to manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent) following the manufacturer’s instruction with minor modifications. Briefly, 0.4 µg RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporated a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTPs (Perkin Elmer). RNA spike-in controls (Agilent) were added to RNA samples before amplification and labeling. The labeled cRNA was purified using RNeasy mini kit (Qiagen).
|
| |
|
| Hybridization protocol |
Total 0.825 µg of each Cy3-labeled sample was used for hybridization on Agilent 4x 44K whole human genome microarray at 65ºC for 17 hours in a hybridization oven with rotation.
|
| Scan protocol |
Slides were scanned using the Agilent Microarray Scanner controlled by Agilent Scan Control 7.0 software.
|
| Description |
N4
|
| Data processing |
Microarray data were extracted with Agilent Feature Extraction 9.5.3.1 software and imported into GeneSpring GX 9.0.1 (Agilent). Normalization was done with all intensities higher than 5, log2 transformation and cross-array quartile normalization. Features with intensities smaller than 300 at all time points were excluded from the analysis.
|
| |
|
| Submission date |
Dec 10, 2008 |
| Last update date |
Dec 10, 2008 |
| Contact name |
Jin Song |
| E-mail(s) |
jsong20@jhmi.edu
|
| Phone |
4105020419
|
| Fax |
410-502-7882
|
| Organization name |
Johns Hopkins Medical Institutions
|
| Department |
Pathology
|
| Lab |
Center for Biomarker Discovery
|
| Street address |
419 N. Caroline Str.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE13893 |
Dynamic response of annexin A11-associated gene expression to cisplatin treatment |
|
