|
| Status |
Public on Oct 19, 2011 |
| Title |
Uvect-UERG Rep 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Immortalized cell line
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: RWPE-1 cells expressing Flag-ERG, treated with U0126.
cell line: RWPE-1
vector: Flag-ERG
treatment: U0126
|
| Treatment protocol |
Indicated samples were treated with 10 micromolar U0126 for six hours prior to harvesting RNA
|
| Growth protocol |
RWPE-1 cells were maintained in Keratinocyte Serum Free media with EGF and bovine pituitary extract supplements (Invitrogen)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit with on column DNase digestion
|
| Label |
Cy3
|
| Label protocol |
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| |
|
| Channel 2 |
| Source name |
Immortalized cell line
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: RWPE-1 cells expressing empty vector, treated with U0126.
cell line: RWPE-1
vector: empty
treatment: U0126
|
| Treatment protocol |
Indicated samples were treated with 10 micromolar U0126 for six hours prior to harvesting RNA
|
| Growth protocol |
RWPE-1 cells were maintained in Keratinocyte Serum Free media with EGF and bovine pituitary extract supplements (Invitrogen)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit with on column DNase digestion
|
| Label |
Cy5
|
| Label protocol |
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| |
|
| |
| Hybridization protocol |
Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com
|
| Scan protocol |
Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.
|
| Description |
Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
|
| Data processing |
Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.
|
| |
|
| Submission date |
May 21, 2011 |
| Last update date |
Jun 25, 2012 |
| Contact name |
Jacqueline Lopez |
| E-mail(s) |
[email protected]
|
| Phone |
574-631-1902
|
| Organization name |
University of Notre Dame
|
| Department |
Biology
|
| Lab |
Pfrender Laboratory
|
| Street address |
019 Galvin Life Science Center
|
| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL13635 |
| Series (1) |
| GSE29438 |
Oncogenic ETS proteins regulate a Ras/MAPK gene expression program in the absence of MAPK signaling |
|
