|
| Status |
Public on Sep 25, 2014 |
| Title |
OCI-LY3, Rapamycin, 22 uM, 12hrs, Replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 22 uM concentration
|
| Organism |
Homo sapiens |
| Characteristics |
drug: Rapamycin
concentration: 22 uM
time point: 12hrs
replicate: 1
|
| Treatment protocol |
Cells were seeded at 5x10^4 cells/well in 96-well culture plates and 12 hrs post-plating were treated with the specified drug. Samples were harvested in triplicate at 6, 12 and 24 hours post compound addition. In each experiment, vehicle (DMSO)-treated samples were used as controls.
|
| Growth protocol |
OCI-LY3 cells were cultured under standard conditions in IMDM supplemented with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each well on an automated liquid handling system using the RNAqueous-96 Automated Kit (Ambion) following the manufacturer’s instructions. RNA quantification was performed by NanoDrop 8000 spectrophotometer and itd integrity evaluated by Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
cRNA synthesis and biotin-labelling was performed starting with 300 ng of total RNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) following manufacterer's protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 7.5 ug of cRNA were hybridized on HG-U219 arrays in 120ul volume/well. The GeneTitan Hybridization, Wash and Stain kit (Affymetrix) was used for preparing hybridization mixes and automated processing of 96-array plates on the GeneTitan Instrument (Affymetrix).
|
| Scan protocol |
HG-U219 Array Plates were scanned on the GeneTitan instrument (Affymetrix) imaging device according to manufacturer's instructions.
|
| Description |
OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 22 uM concentration
|
| Data processing |
Determination of the signal values were obtained with GeneChip Command Console Software (AGCC) (Affymetrix). Raw data were normalized with the Robust Multichip Analysis (RMA) algorithm using BioConductor Affy Package. Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
Sep 25, 2014 |
| Contact name |
Mukesh Bansal |
| Organization name |
Columbia University
|
| Street address |
1130 St. Nicholas Ave. Room 908
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE51068 |
High-throughput expression profiling of OCI-Ly3 cell line upon treatment with a panel of 14 known drugs. |
|
