|
| Status |
Public on Jul 08, 2015 |
| Title |
DMSO_OCI-Ly7_24_TH001_NG_101118_05_H01 |
| Sample type |
RNA |
| |
|
| Source name |
OCI-Ly7
|
| Organism |
Homo sapiens |
| Characteristics |
compound treated: DMSO
cell line: OCI-Ly7
time: 24 hrs
|
| Treatment protocol |
A stock concentration of the IC20 at 24 hour was created by dilution in DMSO. Cells were treated with the 24hr IC20 of each of the compounds for 6, 12, and 24hrs at 37°C, 5% CO2 under humidified conditions. 0.2% DMSO vehicle treated samples were used as controls.
|
| Growth protocol |
Cell lines were cultured in Iscove’s Modified Dulbecco Medium supplemented with 10% fetal bovine serum at 37°C in a 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNAqueous-96 Automated Kit (Ambion) on the Janus automated liquid handling system (Perkin Elmer Inc.), quantified by NanoDrop 6000 spectrophotometer and quality checked by Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
300ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol
|
| |
|
| Hybridization protocol |
Following fragmentation with a buffered zinc solution (Fragmentation Reagent, Ambion), 7.5 ug of labelled 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 processing of 96-array plates on the GeneTitan Instrument (Affymetrix).
|
| Scan protocol |
Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions
|
| Description |
tumor cell line
Therasis_Plate12_TH001_NG_20101118_05_H01
|
| Data processing |
The data were analyzed with RMA method in R
|
| |
|
| Submission date |
Aug 13, 2014 |
| Last update date |
Jul 08, 2015 |
| Contact name |
Andrea Califano |
| Organization name |
Columbia University
|
| Street address |
1130 St. Nicholas Avenue, Rm. 906
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE60408 |
Expression profiles in 3 different B-cell lymphoma cell lines treated by 92 FDA approved compounds |
|
