|
| Status |
Public on Apr 30, 2014 |
| Title |
SBC-3 control |
| Sample type |
RNA |
| |
|
| Source name |
lung cancer cells_control vector
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SBC-3
cell type: lung small cell calcinoma
transduced with: control vector (pCMV6-Mock)
time point: 24h after transduction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), according to the protocol provided by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60Karray slides (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides
|
| Description |
SBC-3 control
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10.1.1. (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
Apr 30, 2014 |
| Contact name |
Nozomi Yanagihara |
| E-mail(s) |
yanagihara.nozomi@sapmed.ac.jp
|
| Organization name |
Sapporo Medical University School of Medicine
|
| Department |
Department of Clinical Laboratory Medicine
|
| Street address |
South-1, West-16, Chuo-Ku
|
| City |
Sapporo |
| ZIP/Postal code |
060-8543 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE56595 |
Significance of SALL4 as a drug resistant factor in lung cancer |
|
