|
| Status |
Public on Feb 01, 2011 |
| Title |
GC resistant clone C7H2-R19F2 treated for 6 hours with GC |
| Sample type |
RNA |
| |
|
| Source name |
GC resistant clone C7H2-R19F2 treated for 6 hours with GC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphoblastic leukemia
gc resistant: TRUE
treatment: GC
|
| Treatment protocol |
Cells were treated with 100nM dexametasone (Sigma, Vienna, Austria) or 0.1% ethanol as carrier control.
|
| Growth protocol |
Cell lines were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity. The cells were free of mycoplamsa infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
|
| Label |
biotin
|
| Label protocol |
Total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
|
| |
|
| Hybridization protocol |
20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
|
| Scan protocol |
Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.
|
| Description |
GC resistant clone C7H2-R19F2 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).
|
| Data processing |
The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's gcrma package).
|
| |
|
| Submission date |
Jun 04, 2010 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Johannes Rainer |
| E-mail(s) |
[email protected]
|
| Organization name |
Eurac Researc
|
| Department |
Institute for Biomedicine
|
| Lab |
Biomedical Informatics
|
| Street address |
Via A. Volta 21
|
| City |
Bolzano |
| ZIP/Postal code |
39100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE22152 |
Gene expression data of glucocorticoid resistant and sensitive acute lymphoblastic leukemia cell lines |
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