|
| Status |
Public on Aug 06, 2010 |
| Title |
SRC-5AZA-1 |
| Sample type |
RNA |
| |
|
| Source name |
Swarm Rat chondrosarcoma Cell line treated with 5-aza-2-deoxycytidine
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Rat chondrosarcoma
cell line: Swarm cells
treatment: 0.1uM 5-aza-2-deoxycytidine
|
| Treatment protocol |
Experimental cells: Swarm Rat Chondrosarcoma cells treated with 5-aza-2-deoxycytidine(0.1uM) for five passages.
|
| Growth protocol |
Swarm rat chondrosarcoma cells were cultured in DMEM high glucose (4.5g glucose/ml) supplemented with 10% FBS and Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizo (Invitrogen), RNA was treated with TURBO DNA-free (Ambion).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of Swarm Rat Chondrosarcoma cells treated with 5-aza-2-deoxycytidine for five passages. It is the first of two biologic replicates, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Aug 11, 2009 |
| Last update date |
Aug 18, 2009 |
| Contact name |
Christopher A Hamm |
| Organization name |
Children’s Memorial Research Center
|
| Department |
Cancer Biology and Epigenomics
|
| Lab |
Soares
|
| Street address |
2430 N. Halsted Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60614 |
| Country |
USA |
| |
|
| Platform ID |
GPL8990 |
| Series (1) |
| GSE17598 |
5-aza-2-deoxycytidine treatment of Swarm rat chondrosarcoma cells |
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