|
| Status |
Public on Sep 01, 2010 |
| Title |
U937 transfected with control GFP, 6 hours post transfection, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
U937 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937 cells
transfectant: transfected with plasmid containing control GFP
|
| Treatment protocol |
Transfection of pEGFP, pEGFP-PRWT and pEGFP-PR2VR in U937 cells was performed by electroporation (BTX).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
|
| |
|
| Hybridization protocol |
15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
|
| Scan protocol |
Gene chips were scanned using GS3000.
|
| Data processing |
To perform inter-array comparisons, the raw data for each array were scaled to an average intensity of 1,500 with Affymetrix Microarray Suite software and the (MAS5) statistical algorithm. Probesets were filtered to remove those that did not have at least 2 present calls in at least 1 of the groups (GFP, GFP-PR, GFP-PR_2VR). The remaining probesets were subjected to ANOVA, with differentially expressed genes defined at a significance level of p<0.01. MAS5-generated signal intensities were normalized to z-scores for hierarchical clustering and heatmap creation only. Statistical analysis, hierarchical clustering, and creation of heat maps were performed with Spotfire software (Spotfire, Somerville, MA).
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| |
|
| Submission date |
Apr 27, 2010 |
| Last update date |
Apr 27, 2010 |
| Contact name |
Rekha Meyer |
| E-mail(s) |
rmeyer@pathbox.wustl.edu
|
| Phone |
314 362 8853
|
| Organization name |
Washington University School of Medicine
|
| Street address |
4320 Forest Park Av
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63128 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE21550 |
Effect of Protease-resistant PML-RARĪ± on the leukemogenic potential in a mouse model of Acute Promyelocytic Leukemia |
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