|
| Status |
Public on Apr 06, 2011 |
| Title |
20913_RA8h_2 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: glioblastoma neurospheres
cell line: 20913
treatment group: retinoic acid for 8h
|
| Treatment protocol |
All-trans retinoic acid (RA) was prepared as stock solutions in DMSO and diluted in cell culture medium to the final concentration of 10 uM. In all the experiments, the final DMSO concentration was < 0.1%.
|
| Growth protocol |
The human glioblastoma neurosphere lines HSR-GBM1A (20913) and HSR-GBM 1B (10627) were originally derived by Vescovi and colleagues and maintained in serum-free medium supplemented with EGF and FGF. Cells were incubated in a humidified incubator containing 5% CO2/95% air at 37°C, and passaged every 4-5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy kit from Qiagen
|
| Label |
Biotin
|
| Label protocol |
Single-strand cDNA was generated from the amplified cRNA, fragmented and labeled following Affymetrix Whole Transcript Sense Target Labeling Assay Manual (Rev. 5). Sample labeling, hybridization, and scanning was carried out in JHMI microarray core facility.
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix GeneChip Human Exon 1.0ST. Arrays was carried out in Affymetrix hybridization Oven 640 following Affymetrix Whole Transcript sense Target Labeling Assay Manual (Rev. 5).
|
| Scan protocol |
Array was scanned using Affymetrix GeneChip Scanner 3000 with G7 upgrade according to the manufacturer's recommendation. Array was scanned using Affymetrix GeneChip Scanner 3000 with G7 upgrade according to the manufacturer's recommendation.
|
| Description |
RNA expression value
Sxia_GBM-SC-20913-RA8h_2a_Huexon.CEL
|
| Data processing |
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and quantile normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
The probe group report file (SXio032409_Report.txt) and processed data file with full header (rma-gene-extended.summary.txt) are available as supplementary files on the Series record.
|
| |
|
| Submission date |
Apr 14, 2010 |
| Last update date |
Apr 06, 2011 |
| Contact name |
Shuli Xia |
| E-mail(s) |
[email protected]
|
| Phone |
443-923-2683
|
| Organization name |
Kennedy-Krieger Institute
|
| Street address |
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE21336 |
GBM_SC_retinoic acid_gene_expression |
|
