|
| Status |
Public on Jul 22, 2011 |
| Title |
CPT 2 h |
| Sample type |
RNA |
| |
|
| Source name |
HCT116 cells treated with 10 μM CPT during 2 h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colon carcinoma cells
cell line: HCT116
treatment group: treated with 10 μM CPT during 2 h
|
| Treatment protocol |
HCT116 cells were treated with CPT for 1, 2, 4, 15 and 20 hours. Controls samples were analyzed at 4 and 20 h following DMSO treatment (0.1%; the solvent used to dissolve CPT).
|
| Growth protocol |
Human HCT116 cell line was obtained from ATCC (Rockville, MD) and grown in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gemini Bio-products, West Sacramento, CA) at 37 degrees Celsius in 95% air and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with the “Nucleospin RNA II” kit (Macherey-Nagel, Bethlehem, PA).
|
| Label |
biotin
|
| Label protocol |
Sample amplification and labeling was performed using the WT-Ovation Pico RNA Amplification System and the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., part # 's 3300-60 and 4200-60) according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays. The arrays were washed and stained using the FS450-0001 Fluidics protocol.
|
| Scan protocol |
The scanning was done using the Affymetrix GeneChip® Scanner 3000 7G.
|
| Description |
HCT116 cells treated with 10 μM CPT during 2 h
|
| Data processing |
The probe level normalization using RMA was done using Partek Genomics Suite v6.08 and the summarization of the probes was done on R 2.11.1.
|
| |
|
| Submission date |
Aug 17, 2010 |
| Last update date |
Jul 23, 2011 |
| Contact name |
Jennifer Barb |
| E-mail(s) |
[email protected]
|
| Phone |
3014359232
|
| Organization name |
NIH
|
| Department |
DCB
|
| Lab |
MSCL
|
| Street address |
12 South Drive Bldg 12A Room 2001
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL7884 |
| Series (1) |
| GSE23677 |
Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors |
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