|
| Status |
Public on Jul 28, 2018 |
| Title |
A498 DGAT1/2 shRNA cells, doxycycline treatment, hypoxia, biol repl 3 |
| Sample type |
RNA |
| |
|
| Source name |
A498 expressing induced DGAT1/2 shRNA construct grown under serum deprivation and hypoxia
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: doxycycline
cell line: A498
cell type: Clear cell renal cell carcinoma (ccRCC)
genotype/variation: DGAT1/2 knockdown
oxygen levels: hypoxia
|
| Treatment protocol |
Vehicle/Doxycycline treatment was applied for 5 days and normoxic/hypoxic treatment was applied for 2 days before RNA extraction
|
| Growth protocol |
Low serum growth conditions. Vehicle/Doxycycline treatment was applied for 5 days and normoxic/hypoxic treatment was applied for 2 days before RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extraction was performed with RNEasy columns according to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
250ng of total RNA was converted to biotinylated cDNA using standard protocols used by the Molecular Profiling Core at the University of Pennsylvania
|
| |
|
| Hybridization protocol |
Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
|
| Scan protocol |
A GeneChip 3000 7G scanner was used to collect fluorescence signal.
|
| Data processing |
RMA-sst was applied using Affymetroix Transcriptome Analysis Console (TAC) with default settings
|
| |
|
| Submission date |
Jul 27, 2018 |
| Last update date |
Jul 28, 2018 |
| Contact name |
Daniel Ackerman |
| E-mail(s) |
[email protected]
|
| Phone |
2155739755
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Blvd, BRB II/III, Rm 646
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE117775 |
Effect of DGAT loss on hypoxic tumor cells growing under serum-deprived conditions |
|
