|
| Status |
Public on Feb 01, 2011 |
| Title |
Epilepsy patient E3, 2 hours GC treatment |
| Sample type |
RNA |
| |
|
| Source name |
Mononuclear cells, epilepsy patient E3, 2 hours after GC administration
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 2 hrs
patient: E3
|
| Treatment protocol |
Single administration of the glucocorticoid dexamethasone (20 mg/m2).
|
| Growth protocol |
None.
|
| 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, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
|
| Label |
biotin
|
| Label protocol |
1ug 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 was performed with the GCOS (version 1.4.0.036) software.
|
| Description |
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 2 hours after GC administration.
E3-2h
|
| Data processing |
The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
|
| |
|
| Submission date |
Jul 06, 2010 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Johannes Rainer |
| E-mail(s) |
johannes.rainer@eurac.edu
|
| 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) |
| GSE22779 |
Gene expression data of non-leukemic individuals before and during in-vivo glucocorticoid treatment |
|
